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A mitochondrial cytochrome P-450 that catalyzes multiple oxidation reaction in bile acid biosynthesis.", - "textContent": "12", + "textContent": "29", "type": [ "PublicationXref", "PubMed:1708392" @@ -33205,7 +33205,7 @@ "id": "publicationXrefa3e", "source": "Biochim Biophys Acta", "standardName": "Modification of low-density lipoprotein by myeloperoxidase-derived oxidants and reagent hypochlorous acid.", - "textContent": "59", + "textContent": "127", "type": [ "PublicationXref", "PubMed:16698314" @@ -33223,7 +33223,7 @@ "id": "publicationXrefa3f", "source": "J Biol Chem", "standardName": "Selenoproteins.", - "textContent": "242", + "textContent": "250", "type": [ "PublicationXref", "PubMed:18757362" @@ -33245,7 +33245,7 @@ "id": "publicationXrefa40", "source": "Biol Trace Elem Res", "standardName": "Serum selenium concentrations correlate significantly with inflammatory biomarker high-sensitive CRP levels in Hungarian gestational diabetic and healthy pregnant women at mid-pregnancy.", - "textContent": "311", + "textContent": "322", "type": [ "PublicationXref", "PubMed:17960332" @@ -33266,7 +33266,7 @@ "id": "publicationXrefa41", "source": "Biochim Biophys Acta", "standardName": "Identification of the GGPS1 genes encoding geranylgeranyl diphosphate synthases from mouse and human.", - "textContent": "31", + "textContent": "264", "type": [ "PublicationXref", "PubMed:10101267" @@ -33285,7 +33285,7 @@ "id": "publicationXrefa46", "source": "J Physiol Pharmacol", "standardName": "Nitric oxide and superoxide in inflammation and immune regulation.", - "textContent": "212", + "textContent": "310", "type": [ "PublicationXref", "PubMed:14726604" @@ -33303,7 +33303,7 @@ "id": "publicationXrefa48", "source": "Proc Natl Acad Sci U S A", "standardName": "Inhibition of arachidonate 5-lipoxygenase triggers massive apoptosis in human prostate cancer cells.", - "textContent": "193", + "textContent": "55", "type": [ "PublicationXref", "PubMed:9789062" @@ -33324,7 +33324,7 @@ "id": "publicationXrefa49", "source": "Biochemistry.", "standardName": "Binding of Pyridoxal 5'-Phosphate to the Heme Protein Human Cystathionine -Synthase", - "textContent": "24", + "textContent": "54", "type": [ "PublicationXref" ], @@ -33343,7 +33343,7 @@ "id": "publicationXrefa4a", "source": "Antioxid Redox Signal", "standardName": "Structure-function relationships, physiological roles and evolution of mammalian ER-resident selenoproteins.", - "textContent": "328", + "textContent": "156", "type": [ "PublicationXref", "PubMed:19747065" @@ -33365,7 +33365,7 @@ "id": "publicationXrefa4c", "source": "J Biol Chem", "standardName": "Suppression of leukotriene formation in RBL-2H3 cells that overexpressed phospholipid hydroperoxide glutathione peroxidase.", - "textContent": "278", + "textContent": "199", "type": [ "PublicationXref", "PubMed:9442035" @@ -33385,7 +33385,7 @@ "id": "publicationXrefa53", "source": "Antioxid Redox Signal", "standardName": "From selenium to selenoproteins: synthesis, identity, and their role in human health.", - "textContent": "66", + "textContent": "184", "type": [ "PublicationXref", "PubMed:17508906" @@ -33406,7 +33406,7 @@ "id": "publicationXrefa54", "source": "Science", "standardName": "Kappa B-specific DNA binding proteins: role in the regulation of human interleukin-2 gene expression.", - "textContent": "265", + "textContent": "23", "type": [ "PublicationXref", "PubMed:2497518" @@ -33426,7 +33426,7 @@ "id": "publicationXrefa58", "source": "IUBMB Life.", "standardName": "Is alpha-lipoic acid a scavenger of reactive oxygen species in vivo? Evidence for its initiation of stress signaling pathways that promote endogenous antioxidant capacity.", - "textContent": "147", + "textContent": "145", "type": [ "PublicationXref", "PubMed:18409172" @@ -33444,7 +33444,7 @@ "id": "publicationXrefa62", "source": "Biochem Pharmacol.", "standardName": "The isoprostanes. Current knowledge and directions for future research.", - "textContent": "272", + "textContent": "179", "type": [ "PublicationXref", "PubMed:8534261" @@ -33461,7 +33461,7 @@ "id": "publicationXrefa64", "source": "Am J Clin Nutr", "standardName": "Vitamin B-12: plant sources, requirements, and assay.", - "textContent": "178", + "textContent": "189", "type": [ "PublicationXref", "PubMed:3046314" @@ -33482,7 +33482,7 @@ "id": "publicationXrefa6d", "source": "Proc Natl Acad Sci U S A", "standardName": "Triene prostaglandins: prostacyclin and thromboxane biosynthesis and unique biological properties.", - "textContent": "167", + "textContent": "9", "type": [ "PublicationXref", "PubMed:218223" @@ -33502,7 +33502,7 @@ "id": "publicationXrefa7c", "source": "Hum Mol Genet", "standardName": "Molecular basis for methionine synthase reductase deficiency in patients belonging to the cblE complementation group of disorders in folate/cobalamin metabolism.", - "textContent": "282", + "textContent": "202", "type": [ "PublicationXref", "PubMed:10484769" @@ -33523,7 +33523,7 @@ "id": "publicationXrefa86", "source": "J Immunol", "standardName": "Inhibition of TLR activation and up-regulation of IL-1R-associated kinase-M expression by exogenous gangliosides.", - "textContent": "75", + "textContent": "147", "type": [ "PublicationXref", "PubMed:18354163" @@ -33548,7 +33548,7 @@ "id": "publicationXrefa87", "source": "Am J Hum Genet", "standardName": "Mutations in the 3beta-hydroxysterol Delta24-reductase gene cause desmosterolosis, an autosomal recessive disorder of cholesterol biosynthesis.", - "textContent": "39", + "textContent": "80", "type": [ "PublicationXref", "PubMed:11519011" @@ -33568,7 +33568,7 @@ "id": "publicationXrefa89", "source": "Endocr Rev", "standardName": "Selenium, the thyroid, and the endocrine system.", - "textContent": "299", + "textContent": "106", "type": [ "PublicationXref", "PubMed:16174820" @@ -33587,7 +33587,7 @@ "id": "publicationXrefa8b", "source": "Arch Biochem Biophys", "standardName": "Cloning, heterologous expression, and enzymological characterization of human squalene monooxygenase.", - "textContent": "110", + "textContent": "68", "type": [ "PublicationXref", "PubMed:10666321" @@ -33614,7 +33614,7 @@ "id": "publicationXrefa8e", "source": "Am J Hum Genet", "standardName": "Smith-Lemli-Opitz syndrome is caused by mutations in the 7-dehydrocholesterol reductase gene.", - "textContent": "196", + "textContent": "262", "type": [ "PublicationXref", "PubMed:9683613" @@ -33656,7 +33656,7 @@ "id": "publicationXrefa9f", "source": "Transplantation", "standardName": "Dietary selenium increases cellular glutathione peroxidase activity and reduces the enhanced susceptibility to lipid peroxidation of plasma and low-density lipoprotein in kidney transplant recipients.", - "textContent": "18", + "textContent": "47", "type": [ "PublicationXref", "PubMed:9075838" @@ -33673,7 +33673,7 @@ "id": "publicationXrefaa7", "source": "Biochim Biophys Acta", "standardName": "Methionine oxidation by reactive oxygen species: reaction mechanisms and relevance to Alzheimer's disease.", - "textContent": "53", + "textContent": "113", "type": [ "PublicationXref", "PubMed:15680219" @@ -33693,7 +33693,7 @@ "id": "publicationXrefaa9", "source": "J Am Diet Assoc", "standardName": "Genetic variants in phosphatidylethanolamine N-methyltransferase and methylenetetrahydrofolate dehydrogenase influence biomarkers of choline metabolism when folate intake is restricted.", - "textContent": "327", + "textContent": "290", "type": [ "PublicationXref", "PubMed:19167960" @@ -33713,7 +33713,7 @@ "id": "publicationXrefaac", "source": "Biochim Biophys Acta", "standardName": "Modification of low-density lipoprotein by myeloperoxidase-derived oxidants and reagent hypochlorous acid.", - "textContent": "229", + "textContent": "124", "type": [ "PublicationXref", "PubMed:16698314" @@ -33732,7 +33732,7 @@ "id": "publicationXrefab2", "source": "Biochem Cell Biol", "standardName": "Metabolic and molecular aspects of ethanolamine phospholipid biosynthesis: the role of CTP:phosphoethanolamine cytidylyltransferase (Pcyt2).", - "textContent": "307", + "textContent": "231", "type": [ "PublicationXref", "PubMed:17612623" @@ -33751,7 +33751,7 @@ "id": "publicationXrefab5", "source": "J Biol Chem", "standardName": "Human lysophosphatidic acid acyltransferase. cDNA cloning, expression, and localization to chromosome 9q34.3.", - "textContent": "19", + "textContent": "303", "type": [ "PublicationXref", "PubMed:9242711" @@ -33770,7 +33770,7 @@ "id": "publicationXrefab8", "source": "Proc Natl Acad Sci U S A", "standardName": "Squalene synthetase activity in human fibroblasts: regulation via the low density lipoprotein receptor.", - "textContent": "168", + "textContent": "8", "type": [ "PublicationXref", "PubMed:228272" @@ -33789,7 +33789,7 @@ "id": "publicationXrefabc", "source": "Biochem Biophys Res Commun", "standardName": "Efficient reduction of lipoamide and lipoic acid by mammalian thioredoxin reductase.", - "textContent": "273", + "textContent": "178", "type": [ "PublicationXref", "PubMed:8769129" @@ -33806,7 +33806,7 @@ "id": "publicationXrefac7", "source": "Free Radic Biol Med", "standardName": "Tetrahydrobiopterin, superoxide, and vascular dysfunction.", - "textContent": "243", + "textContent": "162", "type": [ "PublicationXref", "PubMed:19628033" @@ -33823,7 +33823,7 @@ "id": "publicationXrefad3", "source": "Biol Chem", "standardName": "Glutathione peroxidases and redox-regulated transcription factors.", - "textContent": "303", + "textContent": "123", "type": [ "PublicationXref", "PubMed:17081103" @@ -33841,7 +33841,7 @@ "id": "publicationXrefad8", "source": "Proc Natl Acad Sci U S A", "standardName": "The extremely slow and variable activity of dihydrofolate reductase in human liver and its implications for high folic acid intake.", - "textContent": "83", + "textContent": "289", "type": [ "PublicationXref", "PubMed:19706381" @@ -33862,7 +33862,7 @@ "id": "publicationXrefadb", "source": "J Biol Chem", "standardName": "Expression cloning of a human cDNA restoring sphingomyelin synthesis and cell growth in sphingomyelin synthase-defective lymphoid cells.", - "textContent": "50", + "textContent": "102", "type": [ "PublicationXref", "PubMed:14976195" @@ -33879,7 +33879,7 @@ "id": "publicationXrefadd", "source": "Prostaglandins Other Lipid Mediat", "standardName": "Prostaglandin F synthase.", - "textContent": "42", + "textContent": "86", "type": [ "PublicationXref", "PubMed:12432932" @@ -33903,7 +33903,7 @@ "id": "publicationXrefade", "source": "Free Radic Biol Med", "standardName": "Blocking tumor cell eicosanoid synthesis by GP x 4 impedes tumor growth and malignancy.", - "textContent": "139", + "textContent": "282", "type": [ "PublicationXref", "PubMed:16413410" @@ -33923,7 +33923,7 @@ "id": "publicationXrefae0", "source": "FEBS Lett", "standardName": "Cloning of a human choline kinase cDNA by complementation of the yeast cki mutation.", - "textContent": "268", + "textContent": "30", "type": [ "PublicationXref", "PubMed:1618328" @@ -33941,7 +33941,7 @@ "id": "publicationXrefae2", "source": "Pharmacol Res", "standardName": "Oxidative stress in normal and impaired wound repair.", - "textContent": "153", + "textContent": "148", "type": [ "PublicationXref", "PubMed:18617006" @@ -33961,7 +33961,7 @@ "id": "publicationXrefae3", "source": "J Biol Chem", "standardName": "Selenoprotein H is a redox-sensing high mobility group family DNA-binding protein that up-regulates genes involved in glutathione synthesis and phase II detoxification.", - "textContent": "64", + "textContent": "132", "type": [ "PublicationXref", "PubMed:17526492" @@ -33981,7 +33981,7 @@ "id": "publicationXrefae5", "source": "J Lipid Res", "standardName": "Characterization of phosphomevalonate kinase: chromosomal localization, regulation, and subcellular targeting.", - "textContent": "199", + "textContent": "266", "type": [ "PublicationXref", "PubMed:10191291" @@ -34009,7 +34009,7 @@ "id": "publicationXrefae8", "source": "Nutrition", "standardName": "Association between dietary fiber and markers of systemic inflammation in the Women's Health Initiative Observational Study.", - "textContent": "236", + "textContent": "151", "type": [ "PublicationXref", "PubMed:18562168" @@ -34027,7 +34027,7 @@ "id": "publicationXrefaea", "source": "J Lipid Res", "standardName": "Cholesterol 7 alpha-hydroxylase from human liver: partial purification and reconstruction into defined phospholipid-cholesterol vesicles.", - "textContent": "171", + "textContent": "10", "type": [ "PublicationXref", "PubMed:7288293" @@ -34047,7 +34047,7 @@ "id": "publicationXrefaeb", "source": "J Biol Chem", "standardName": "The role of CDP-diacylglycerol synthetase and phosphatidylinositol synthase activity levels in the regulation of cellular phosphatidylinositol content.", - "textContent": "99", + "textContent": "261", "type": [ "PublicationXref", "PubMed:9407135" @@ -34074,7 +34074,7 @@ "id": "publicationXrefaf0", "source": "FEBS Lett", "standardName": "Identification and characterization of selenoprotein K: an antioxidant in cardiomyocytes.", - "textContent": "141", + "textContent": "224", "type": [ "PublicationXref", "PubMed:16962588" @@ -34092,7 +34092,7 @@ "id": "publicationXrefaf3", "source": "Antioxid Redox Signal", "standardName": "The covalent FAD of monoamine oxidase: structural and functional role and mechanism of the flavinylation reaction.", - "textContent": "289", + "textContent": "82", "type": [ "PublicationXref", "PubMed:11761328" @@ -34109,7 +34109,7 @@ "id": "publicationXrefaf4", "source": "Haemostasis", "standardName": "Does inflammation contribute to thrombotic events?", - "textContent": "200", + "textContent": "183", "type": [ "PublicationXref", "PubMed:11251339" @@ -34129,7 +34129,7 @@ "id": "publicationXrefaf6", "source": "Proc Natl Acad Sci U S A", "standardName": "IRF-3-dependent, NFkappa B- and JNK-independent activation of the 561 and IFN-beta genes in response to double-stranded RNA.", - "textContent": "44", + "textContent": "208", "type": [ "PublicationXref", "PubMed:11972054" @@ -34146,7 +34146,7 @@ "id": "publicationXrefaf8", "source": "Mol Genet Metab", "standardName": "Folic acid: nutritional biochemistry, molecular biology, and role in disease processes.", - "textContent": "109", + "textContent": "69", "type": [ "PublicationXref", "PubMed:11001804" @@ -34165,7 +34165,7 @@ "id": "publicationXrefaf9", "source": "Biochim Biophys Acta", "standardName": "Heterogeneity and function of mammalian MSRs: enzymes for repair, protection and regulation.", - "textContent": "54", + "textContent": "112", "type": [ "PublicationXref", "PubMed:15680232" @@ -34188,7 +34188,7 @@ "id": "publicationXrefafb", "source": "J Biol Chem", "standardName": "Molecular cloning of human mevalonate kinase and identification of a missense mutation in the genetic disease mevalonic aciduria.", - "textContent": "267", + "textContent": "176", "type": [ "PublicationXref", "PubMed:1377680" @@ -34205,7 +34205,7 @@ "id": "publicationXrefafd", "source": "Nutrition", "standardName": "Folic acid says NO to vascular diseases.", - "textContent": "295", + "textContent": "96", "type": [ "PublicationXref", "PubMed:12831960" @@ -34222,7 +34222,7 @@ "id": "publicationXrefaff", "source": "Biochim Biophys Acta", "standardName": "Methionine oxidation by reactive oxygen species: reaction mechanisms and relevance to Alzheimer's disease.", - "textContent": "227", + "textContent": "218", "type": [ "PublicationXref", "PubMed:15680219" @@ -34240,7 +34240,7 @@ "id": "publicationXrefb05", "source": "J Lipid Res", "standardName": "Influence of the amino acid moiety on deconjugation of bile acid amidates by cholylglycine hydrolase or human fecal cultures.", - "textContent": "263", + "textContent": "21", "type": [ "PublicationXref", "PubMed:2876046" @@ -34257,7 +34257,7 @@ "id": "publicationXrefb1c", "source": "Clin Rev Allergy Immunol", "standardName": "Oxidative modification of LDL: its pathological role in atherosclerosis.", - "textContent": "157", + "textContent": "166", "type": [ "PublicationXref", "PubMed:18987785" @@ -34280,7 +34280,7 @@ "id": "publicationXrefb1f", "source": "Biochem J", "standardName": "Differential metabolism of dihomo-gamma-linolenic acid and arachidonic acid by cyclo-oxygenase-1 and cyclo-oxygenase-2: implications for cellular synthesis of prostaglandin E1 and prostaglandin E2.", - "textContent": "43", + "textContent": "87", "type": [ "PublicationXref", "PubMed:11939906" @@ -34301,7 +34301,7 @@ "id": "publicationXrefb21", "source": "J Mol Biol", "standardName": "Structure and mechanism of a eukaryotic FMN adenylyltransferase.", - "textContent": "247", + "textContent": "329", "type": [ "PublicationXref", "PubMed:19375431" @@ -34322,7 +34322,7 @@ "id": "publicationXrefb2a", "source": "Mol Genet Metab", "standardName": "Altered folate metabolism and disposition in mothers affected by a spina bifida pregnancy: influence of 677c -->t methylenetetrahydrofolate reductase and 2756a -->g methionine synthase genotypes.", - "textContent": "108", + "textContent": "65", "type": [ "PublicationXref", "PubMed:10833329" @@ -34339,7 +34339,7 @@ "id": "publicationXrefb30", "source": "Biochem Pharmacol", "standardName": "New aspects of the role of hydroxyeicosatetraenoic acids in cell growth and cancer development.", - "textContent": "238", + "textContent": "157", "type": [ "PublicationXref", "PubMed:18761324" @@ -34357,7 +34357,7 @@ "id": "publicationXrefb35", "source": "Biochem J", "standardName": "Sphingosine 1-phosphate signalling in mammalian cells.", - "textContent": "106", + "textContent": "72", "type": [ "PublicationXref", "PubMed:10880336" @@ -34376,7 +34376,7 @@ "id": "publicationXrefb37", "source": "Biochemistry", "standardName": "Putative helix F contributes to regioselectivity of hydroxylation in mitochondrial cytochrome P450 27A1.", - "textContent": "114", + "textContent": "76", "type": [ "PublicationXref", "PubMed:11412116" @@ -34397,7 +34397,7 @@ "id": "publicationXrefb39", "source": "Free Radic Biol Med", "standardName": "Synergistic inhibition of cyclooxygenase-2 expression by vitamin E and aspirin.", - "textContent": "107", + "textContent": "67", "type": [ "PublicationXref", "PubMed:11121721" @@ -34416,7 +34416,7 @@ "id": "publicationXrefb3f", "source": "Immunol Lett", "standardName": "The role of sphingosine and ceramide kinases in inflammatory responses.", - "textContent": "300", + "textContent": "114", "type": [ "PublicationXref", "PubMed:15585321" @@ -34438,7 +34438,7 @@ "id": "publicationXrefb42", "source": "Proc Natl Acad Sci U S A", "standardName": "The c-rel protooncogene product c-Rel but not NF-kappa B binds to the intronic region of the human interferon-gamma gene at a site related to an interferon-stimulable response element.", - "textContent": "94", + "textContent": "300", "type": [ "PublicationXref", "PubMed:1542667" @@ -34461,7 +34461,7 @@ "id": "publicationXrefb4a", "source": "J Biol Chem", "standardName": "A molecular basis for insulin resistance. Elevated serine/threonine phosphorylation of IRS-1 and IRS-2 inhibits their binding to the juxtamembrane region of the insulin receptor and impairs their ability to undergo insulin-induced tyrosine phosphorylation.", - "textContent": "97", + "textContent": "46", "type": [ "PublicationXref", "PubMed:9368067" @@ -34484,7 +34484,7 @@ "id": "publicationXrefb53", "source": "J Biol Chem", "standardName": "Structures of prostacyclin synthase and its complexes with substrate analog and inhibitor reveal a ligand-specific heme conformation change.", - "textContent": "235", + "textContent": "285", "type": [ "PublicationXref", "PubMed:18032380" @@ -34504,7 +34504,7 @@ "id": "publicationXrefb54", "source": "Clin Chem", "standardName": "Determination of S-adenosylmethionine and S-adenosylhomocysteine in plasma and cerebrospinal fluid by stable-isotope dilution tandem mass spectrometry.", - "textContent": "201", + "textContent": "70", "type": [ "PublicationXref", "PubMed:11017945" @@ -34528,7 +34528,7 @@ "id": "publicationXrefb59", "source": "Crit Care Med", "standardName": "Glucose metabolism and catecholamines.", - "textContent": "65", + "textContent": "230", "type": [ "PublicationXref", "PubMed:17713401" @@ -34550,7 +34550,7 @@ "id": "publicationXrefb5c", "source": "J Biol Chem", "standardName": "Protein kinase Calpha is involved in interferon regulatory factor 3 activation and type I interferon-beta synthesis.", - "textContent": "63", + "textContent": "134", "type": [ "PublicationXref", "PubMed:17296604" @@ -34571,7 +34571,7 @@ "id": "publicationXrefb5e", "source": "Proc Natl Acad Sci U S A", "standardName": "Localization of the gene encoding 3-hydroxy-3-methylglutaryl-coenzyme A synthase to human chromosome 5.", - "textContent": "90", + "textContent": "20", "type": [ "PublicationXref", "PubMed:2870496" @@ -34594,7 +34594,7 @@ "id": "publicationXrefb60", "source": "J Lipid Res", "standardName": "Cloning and characterization of a cDNA encoding human cardiolipin synthase (hCLS1).", - "textContent": "228", + "textContent": "223", "type": [ "PublicationXref", "PubMed:16547353" @@ -34611,7 +34611,7 @@ "id": "publicationXrefb63", "source": "Clin Rev Allergy Immunol", "standardName": "Oxidative modification of LDL: its pathological role in atherosclerosis.", - "textContent": "82", + "textContent": "326", "type": [ "PublicationXref", "PubMed:18987785" @@ -34629,7 +34629,7 @@ "id": "publicationXrefb76", "source": "Antioxid Redox Signal", "standardName": "Selenoproteins and protection against oxidative stress: selenoprotein N as a novel player at the crossroads of redox signalling and calcium homeostasis.", - "textContent": "244", + "textContent": "327", "type": [ "PublicationXref", "PubMed:19769461" @@ -34656,7 +34656,7 @@ "id": "publicationXrefb77", "source": "J Immunol", "standardName": "Alternatively activated myeloid cells limit pathogenicity associated with African trypanosomiasis through the IL-10 inducible gene selenoprotein P.", - "textContent": "316", + "textContent": "146", "type": [ "PublicationXref", "PubMed:18424738" @@ -34682,7 +34682,7 @@ "id": "publicationXrefb78", "source": "Mol Cell Biol", "standardName": "Characterization of a functional NF-kappa B site in the human interleukin 1 beta promoter: evidence for a positive autoregulatory loop.", - "textContent": "183", + "textContent": "31", "type": [ "PublicationXref", "PubMed:8413223" @@ -34699,7 +34699,7 @@ "id": "publicationXrefb83", "source": "Linus Pauling Institute", "standardName": "Folic acid", - "textContent": "158", + "textContent": "251", "type": [ "PublicationXref" ], @@ -34710,7 +34710,7 @@ "id": "publicationXrefb89", "source": "Washington D.C.: National Academies Press", "standardName": "Food and Nutrition Board, Institute of Medicine. Vitamin B6. Dietary Reference Intakes: Thiamin, Riboflavin, Niacin, Vitamin B6, Vitamin B12, Pantothenic Acid, Biotin, and Choline.", - "textContent": "277", + "textContent": "304", "type": [ "PublicationXref" ], @@ -34727,7 +34727,7 @@ "id": "publicationXrefb91", "source": "Biochim Biophys Acta", "standardName": "Formation of 11-hydroxyeicosatetraenoic acid and 15-hydroxyeicosatetraenoic acid in human umbilical arteries is catalyzed by cyclooxygenase.", - "textContent": "7", + "textContent": "173", "type": [ "PublicationXref", "PubMed:3918580" @@ -34748,7 +34748,7 @@ "id": "publicationXrefb93", "source": "Eur J Biochem", "standardName": "Generation of phosphatidic acid during calcium-loading of human erythrocytes. Evidence for a phosphatidylcholine-hydrolyzing phospholipase D.", - "textContent": "270", + "textContent": "32", "type": [ "PublicationXref", "PubMed:8386626" @@ -34768,7 +34768,7 @@ "id": "publicationXrefb9f", "source": "J Trace Elem Med Biol", "standardName": "Selenium status and its correlates in a British national diet and nutrition survey: people aged 65 years and over.", - "textContent": "208", + "textContent": "271", "type": [ "PublicationXref", "PubMed:11878747" @@ -34791,7 +34791,7 @@ "id": "publicationXrefba1", "source": "J Biol Chem", "standardName": "Homocysteine induces programmed cell death in human vascular endothelial cells through activation of the unfolded protein response.", - "textContent": "40", + "textContent": "306", "type": [ "PublicationXref", "PubMed:11447214" @@ -34809,7 +34809,7 @@ "id": "publicationXrefba4", "source": "Cell Cycle", "standardName": "FoxO1 integrates insulin signaling to VLDL production.", - "textContent": "313", + "textContent": "323", "type": [ "PublicationXref", "PubMed:18927507" @@ -34828,7 +34828,7 @@ "id": "publicationXrefba9", "source": "Hoppe Seylers Z Physiol Chem", "standardName": "Metabolism of sphingosine bases. 8. Distribution, isolation and properties of D-3-oxosphinganine reductase. Stereospecificity of the NADPH-dependent reaction of 3-oxodihydrospingosine (2-amino-1-hydroxyoctadecane-3-one).", - "textContent": "85", + "textContent": "169", "type": [ "PublicationXref", "PubMed:4387676" @@ -34849,7 +34849,7 @@ "id": "publicationXrefbac", "source": "Hoppe Seylers Z Physiol Chem", "standardName": "Purification and characterization of amino-acid N-choloyltransferase from human liver.", - "textContent": "175", + "textContent": "17", "type": [ "PublicationXref", "PubMed:6884990" @@ -34874,7 +34874,7 @@ "id": "publicationXrefbbd", "source": "Prostaglandins.", "standardName": "Synthesis and biological activities of leukotriene F4 and leukotriene F4 sulfone", - "textContent": "258", + "textContent": "295", "type": [ "PublicationXref", "PubMed:6300970" @@ -34891,7 +34891,7 @@ "id": "publicationXrefbc0", "source": "Biochim Biophys Acta", "standardName": "Selenoprotein expression and function-Selenoprotein W.", - "textContent": "246", + "textContent": "164", "type": [ "PublicationXref", "PubMed:19464347" @@ -34915,7 +34915,7 @@ "id": "publicationXrefbc1", "source": "Clin Immunol", "standardName": "Reversible severe combined immunodeficiency phenotype secondary to a mutation of the proton-coupled folate transporter.", - "textContent": "330", + "textContent": "241", "type": [ "PublicationXref", "PubMed:19740703" @@ -34932,7 +34932,7 @@ "id": "publicationXrefbc2", "source": "Antioxid Redox Signal", "standardName": "F2-isoprostanes in human health and diseases: from molecular mechanisms to clinical implications.", - "textContent": "315", + "textContent": "238", "type": [ "PublicationXref", "PubMed:18522490" @@ -34952,7 +34952,7 @@ "id": "publicationXrefbc6", "source": "J Biol Chem", "standardName": "Expression of glucosylceramide synthase, converting ceramide to glucosylceramide, confers adriamycin resistance in human breast cancer cells.", - "textContent": "198", + "textContent": "267", "type": [ "PublicationXref", "PubMed:9873062" @@ -34972,7 +34972,7 @@ "id": "publicationXrefbd7", "source": "J Biol Chem", "standardName": "NF-kappaB1 (p50) homodimers differentially regulate pro- and anti-inflammatory cytokines in macrophages.", - "textContent": "230", + "textContent": "225", "type": [ "PublicationXref", "PubMed:16835236" @@ -34991,7 +34991,7 @@ "id": "publicationXrefbdc", "source": "Biochem J", "standardName": "Substrate-specificities of acid and alkaline ceramidases in fibroblasts from patients with Farber disease and controls.", - "textContent": "259", + "textContent": "14", "type": [ "PublicationXref", "PubMed:6814427" @@ -35010,7 +35010,7 @@ "id": "publicationXrefbe4", "source": "Proc Natl Acad Sci U S A", "standardName": "Urinary 8-hydroxy-2'-deoxyguanosine as a biological marker of in vivo oxidative DNA damage.", - "textContent": "180", + "textContent": "174", "type": [ "PublicationXref", "PubMed:2602371" @@ -35036,7 +35036,7 @@ "id": "publicationXrefbe5", "source": "J Lab Clin Med", "standardName": "Diet and lifestyle are associated with serum C-reactive protein concentrations in a population-based study.", - "textContent": "297", + "textContent": "278", "type": [ "PublicationXref", "PubMed:15668660" @@ -35056,7 +35056,7 @@ "id": "publicationXrefbf2", "source": "Mol Cell Biol", "standardName": "Mammalian selenoprotein in which selenocysteine (Sec) incorporation is supported by a new form of Sec insertion sequence element.", - "textContent": "206", + "textContent": "207", "type": [ "PublicationXref", "PubMed:11839807" @@ -35073,7 +35073,7 @@ "id": "publicationXrefbf9", "source": "Mol Aspects Med", "standardName": "Biochemistry of tryptophan in health and disease.", - "textContent": "5", + "textContent": "186", "type": [ "PublicationXref", "PubMed:6371429" @@ -35090,7 +35090,7 @@ "id": "publicationXrefbfe", "source": "J Lipid Res", "standardName": "Lipogenesis in human adipose tissue.", - "textContent": "165", + "textContent": "170", "type": [ "PublicationXref", "PubMed:5637427" @@ -35113,7 +35113,7 @@ "id": "publicationXrefc06", "source": "Science", "standardName": "Characterization of mammalian selenoproteomes.", - "textContent": "46", + "textContent": "91", "type": [ "PublicationXref", "PubMed:12775843" @@ -35136,7 +35136,7 @@ "id": "publicationXrefc0b", "source": "Circulation", "standardName": "Relationships between homocysteine, factor VIIa, and thrombin generation in acute coronary syndromes.", - "textContent": "286", + "textContent": "268", "type": [ "PublicationXref", "PubMed:10653827" @@ -35155,7 +35155,7 @@ "id": "publicationXrefc0f", "source": "Biochem J", "standardName": "Identification and functional characterization of hCLS1, a human cardiolipin synthase localized in mitochondria.", - "textContent": "140", + "textContent": "120", "type": [ "PublicationXref", "PubMed:16716149" @@ -35177,7 +35177,7 @@ "id": "publicationXrefc1b", "source": "Br J Nutr", "standardName": "A network biology model of micronutrient related health", - "textContent": "154", + "textContent": "235", "type": [ "PublicationXref", "PubMed:18598592" @@ -35198,7 +35198,7 @@ "id": "publicationXrefc1e", "source": "Proc Natl Acad Sci U S A.", "standardName": "Selenoprotein R is a zinc-containing stereo-specific methionine sulfoxide reductase.", - "textContent": "118", + "textContent": "209", "type": [ "PublicationXref", "PubMed:11929995" @@ -35222,7 +35222,7 @@ "id": "publicationXrefc22", "source": "Biochem Biophys Res Commun", "standardName": "Rosiglitazone attenuates NF-kappaB-dependent ICAM-1 and TNF-alpha production caused by homocysteine via inhibiting ERK1/2/p38MAPK activation.", - "textContent": "305", + "textContent": "137", "type": [ "PublicationXref", "PubMed:17583675" @@ -35243,7 +35243,7 @@ "id": "publicationXrefc24", "source": "Mol Cell Endocrinol", "standardName": "Structure-function of human 3 alpha-hydroxysteroid dehydrogenases: genes and proteins.", - "textContent": "296", + "textContent": "101", "type": [ "PublicationXref", "PubMed:15026176" @@ -35261,7 +35261,7 @@ "id": "publicationXrefc25", "source": "J Steroid Biochem Mol Biol", "standardName": "Cytochrome P450 CYP27-catalyzed oxidation of C27-steroid into C27-acid.", - "textContent": "184", + "textContent": "177", "type": [ "PublicationXref", "PubMed:7577714" @@ -35284,7 +35284,7 @@ "id": "publicationXrefc28", "source": "J Immunol", "standardName": "Erythromycin differentially inhibits lipopolysaccharide- or poly(I:C)-induced but not peptidoglycan-induced activation of human monocyte-derived dendritic cells.", - "textContent": "223", + "textContent": "217", "type": [ "PublicationXref", "PubMed:16339544" @@ -35303,7 +35303,7 @@ "id": "publicationXrefc29", "source": "Int J Biochem Cell Biol", "standardName": "Serine hydroxymethyltransferase and threonine aldolase: are they identical?", - "textContent": "33", + "textContent": "73", "type": [ "PublicationXref", "PubMed:10716626" @@ -35320,7 +35320,7 @@ "id": "publicationXrefc2b", "source": "J Leukoc Biol", "standardName": "Myeloperoxidase: friend and foe.", - "textContent": "226", + "textContent": "115", "type": [ "PublicationXref", "PubMed:15689384" @@ -35337,7 +35337,7 @@ "id": "publicationXrefc2d", "source": "Future Oncol", "standardName": "Role of the MTHFR polymorphisms in cancer risk modification and treatment.", - "textContent": "81", + "textContent": "155", "type": [ "PublicationXref", "PubMed:19450180" @@ -35357,7 +35357,7 @@ "id": "publicationXrefc31", "source": "Tenn Med", "standardName": "Fructosamine--an underutilized tool in diabetes management: case report and literature review.", - "textContent": "77", + "textContent": "150", "type": [ "PublicationXref", "PubMed:19024248" @@ -35378,7 +35378,7 @@ "id": "publicationXrefc37", "source": "J Pharm Biomed Anal", "standardName": "Simultaneous determination of unbound thyroid hormones in human plasma using high performance frontal analysis with electrochemical detection.", - "textContent": "129", + "textContent": "107", "type": [ "PublicationXref", "PubMed:15925209" @@ -35405,7 +35405,7 @@ "id": "publicationXrefc3a", "source": "Proc Natl Acad Sci U S A", "standardName": "Cloning and mapping of a cDNA for methionine synthase reductase, a flavoprotein defective in patients with homocystinuria.", - "textContent": "22", + "textContent": "49", "type": [ "PublicationXref", "PubMed:9501215" @@ -35426,7 +35426,7 @@ "id": "publicationXrefc47", "source": "Biochem J", "standardName": "Purification and characterization of human phosphatidylserine synthase 1 and 2.", - "textContent": "150", + "textContent": "149", "type": [ "PublicationXref", "PubMed:19014349" @@ -35446,7 +35446,7 @@ "id": "publicationXrefc51", "source": "Biochemistry", "standardName": "Myeloperoxidase metabolizes thiocyanate in a reaction driven by nitric oxide.", - "textContent": "56", + "textContent": "222", "type": [ "PublicationXref", "PubMed:16430221" @@ -35463,7 +35463,7 @@ "id": "publicationXrefc52", "source": "Annu Rev Nutr", "standardName": "Vitamin E regulatory mechanisms.", - "textContent": "67", + "textContent": "135", "type": [ "PublicationXref", "PubMed:17439363" @@ -35482,7 +35482,7 @@ "id": "publicationXrefc53", "source": "Diabetes Care", "standardName": "Serum selenium and diabetes in U.S. adults.", - "textContent": "306", + "textContent": "232", "type": [ "PublicationXref", "PubMed:17392543" @@ -35499,7 +35499,7 @@ "id": "publicationXrefc56", "source": "J Clin Invest", "standardName": "Bile acid synthesis during development. Mitochondrial 12 alpha-hydroxylation in human fetal liver.", - "textContent": "89", + "textContent": "256", "type": [ "PublicationXref", "PubMed:3919061" @@ -35529,7 +35529,7 @@ "id": "publicationXrefc65", "source": "J Clin Invest", "standardName": "Apolipoprotein A-I is a selective target for myeloperoxidase-catalyzed oxidation and functional impairment in subjects with cardiovascular disease.", - "textContent": "52", + "textContent": "216", "type": [ "PublicationXref", "PubMed:15314690" @@ -35547,7 +35547,7 @@ "id": "publicationXrefc68", "source": "Biochim Biophys Acta", "standardName": "Protection against reactive oxygen species by selenoproteins.", - "textContent": "155", + "textContent": "152", "type": [ "PublicationXref", "PubMed:19268692" @@ -35567,7 +35567,7 @@ "id": "publicationXrefc69", "source": "Biochem Biophys Res Commun", "standardName": "The death domain of IRAK-1: an oligomerization domain mediating interactions with MyD88, Tollip, IRAK-1, and IRAK-4.", - "textContent": "143", + "textContent": "136", "type": [ "PublicationXref", "PubMed:17276401" @@ -35587,7 +35587,7 @@ "id": "publicationXrefc6a", "source": "Appl Environ Microbiol", "standardName": "Formation of ursodeoxycholic acid from chenodeoxycholic acid by a 7 beta-hydroxysteroid dehydrogenase-elaborating Eubacterium aerofaciens strain cocultured with 7 alpha-hydroxysteroid dehydrogenase-elaborating organisms.", - "textContent": "173", + "textContent": "15", "type": [ "PublicationXref", "PubMed:6758698" @@ -35605,7 +35605,7 @@ "id": "publicationXrefc6d", "source": "Methods Enzymol", "standardName": "Phospholipase D from rat brain.", - "textContent": "87", + "textContent": "254", "type": [ "PublicationXref", "PubMed:7278682" @@ -35627,7 +35627,7 @@ "id": "publicationXrefc76", "source": "Hum Reprod", "standardName": "Endothelial function in post-menopausal women: effect of folic acid supplementation.", - "textContent": "218", + "textContent": "98", "type": [ "PublicationXref", "PubMed:15016776" @@ -35646,7 +35646,7 @@ "id": "publicationXrefc7a", "source": "Am J Clin Nutr", "standardName": "Studies of biomarker responses to intervention with vitamin B-12: a systematic review of randomized controlled trials.", - "textContent": "239", + "textContent": "163", "type": [ "PublicationXref", "PubMed:19403638" @@ -35666,7 +35666,7 @@ "id": "publicationXrefc7d", "source": "J Biol Chem", "standardName": "Serum amyloid A promotes cholesterol efflux mediated by scavenger receptor B-I.", - "textContent": "128", + "textContent": "109", "type": [ "PublicationXref", "PubMed:16120612" @@ -35687,7 +35687,7 @@ "id": "publicationXrefc82", "source": "J Biol Chem", "standardName": "The selenoenzyme phospholipid hydroperoxide glutathione peroxidase controls the activity of the 15-lipoxygenase with complex substrates and preserves the specificity of the oxygenation products.", - "textContent": "271", + "textContent": "37", "type": [ "PublicationXref", "PubMed:8617728" @@ -35718,7 +35718,7 @@ "id": "publicationXrefc83", "source": "FASEB J", "standardName": "Selenoprotein T is a PACAP-regulated gene involved in intracellular Ca2+ mobilization and neuroendocrine secretion.", - "textContent": "79", + "textContent": "142", "type": [ "PublicationXref", "PubMed:18198219" @@ -35737,7 +35737,7 @@ "id": "publicationXrefc89", "source": "Hoppe Seylers Z Physiol Chem", "standardName": "Biosynthesis of dihydrosphingosine in vitro.", - "textContent": "250", + "textContent": "1", "type": [ "PublicationXref", "PubMed:4386961" @@ -35754,7 +35754,7 @@ "id": "publicationXrefc8e", "source": "Curr Opin Cell Biol", "standardName": "Cyclooxygenases, peroxide tone and the allure of fish oil.", - "textContent": "225", + "textContent": "219", "type": [ "PublicationXref", "PubMed:15780594" @@ -35775,7 +35775,7 @@ "id": "publicationXrefc92", "source": "J Hepatol", "standardName": "Phospholipid transmethylation and choline phosphotransferase in microsomal fraction of human diseased liver.", - "textContent": "262", + "textContent": "19", "type": [ "PublicationXref", "PubMed:3013986" @@ -35787,7 +35787,7 @@ "publicationXrefc93": { "gpmlElementName": "PublicationXref", "id": "publicationXrefc93", - "textContent": "84", + "textContent": "168", "type": [ "PublicationXref" ], @@ -35804,7 +35804,7 @@ "id": "publicationXrefc99", "source": "Biochim Biophys Acta", "standardName": "Phospholipase A(2) activity in non-glycated and glycated low density lipoproteins.", - "textContent": "189", + "textContent": "38", "type": [ "PublicationXref", "PubMed:8652655" @@ -35823,7 +35823,7 @@ "id": "publicationXrefc9b", "source": "J Lipid Res", "standardName": "Acyl-CoA:cholesterol acyltransferase in human small intestine: its activity and some properties of the enzymic reaction.", - "textContent": "3", + "textContent": "11", "type": [ "PublicationXref", "PubMed:6113262" @@ -35850,7 +35850,7 @@ "id": "publicationXrefc9c", "source": "Nat Struct Biol", "standardName": "Mechanism of metal activation of human hematopoietic prostaglandin D synthase.", - "textContent": "292", + "textContent": "212", "type": [ "PublicationXref", "PubMed:12627223" @@ -35873,7 +35873,7 @@ "id": "publicationXrefc9e", "source": "Obesity (Silver Spring)", "standardName": "Basal and Fasting/Refeeding-regulated Tissue Levels of Endogenous PPAR-alpha Ligands in Zucker Rats.", - "textContent": "241", + "textContent": "243", "type": [ "PublicationXref", "PubMed:19521349" @@ -35885,7 +35885,7 @@ "publicationXrefca3": { "gpmlElementName": "PublicationXref", "id": "publicationXrefca3", - "textContent": "76", + "textContent": "167", "type": [ "PublicationXref", "PubMed:8301225" @@ -35901,7 +35901,7 @@ "id": "publicationXrefca8", "source": "Molecular genetics and metabolism", "standardName": "A common variant in methionine synthase reductase combined with low cobalamin (vitamin B12) increases risk for spina bifida.", - "textContent": "30", + "textContent": "59", "type": [ "PublicationXref", "PubMed:10444342" @@ -35920,7 +35920,7 @@ "id": "publicationXrefca9", "source": "Am J Clin Nutr", "standardName": "Studies of biomarker responses to intervention with riboflavin: a systematic review.", - "textContent": "322", + "textContent": "247", "type": [ "PublicationXref", "PubMed:19403631" @@ -35941,7 +35941,7 @@ "id": "publicationXrefcaf", "source": "Eur J Clin Nutr", "standardName": "Association between the intake of vitamins and trace elements from supplements and C-reactive protein: results of the MONICA/KORA Augsburg study.", - "textContent": "71", + "textContent": "140", "type": [ "PublicationXref", "PubMed:17311055" @@ -35960,7 +35960,7 @@ "id": "publicationXrefcb6", "source": "Nat Prod Rep", "standardName": "Properties of an unusual heme cofactor in PLP-dependent cystathionine beta-synthase.", - "textContent": "308", + "textContent": "321", "type": [ "PublicationXref", "PubMed:17534535" @@ -35985,7 +35985,7 @@ "id": "publicationXrefcb9", "source": "J Immunol", "standardName": "Inhibition of human neutrophil superoxide generation by alpha 1-antichymotrypsin.", - "textContent": "13", + "textContent": "28", "type": [ "PublicationXref", "PubMed:1848582" @@ -36012,7 +36012,7 @@ "id": "publicationXrefcbc", "source": "Proc Natl Acad Sci U S A", "standardName": "Identification of a novel selD homolog from eukaryotes, bacteria, and archaea: is there an autoregulatory mechanism in selenocysteine metabolism?", - "textContent": "96", + "textContent": "192", "type": [ "PublicationXref", "PubMed:8986768" @@ -36034,7 +36034,7 @@ "id": "publicationXrefcbd", "source": "Nat Struct Biol.", "standardName": "Domain alternation switches B(12)-dependent methionine synthase to the activation conformation.", - "textContent": "207", + "textContent": "88", "type": [ "PublicationXref", "PubMed:11731805" @@ -36060,7 +36060,7 @@ "id": "publicationXrefcc4", "source": "Hum Mol Genet.", "standardName": "Human methionine synthase: cDNA cloning and identification of mutations in patients of the cblG complementation group of folate/cobalamin disorders.", - "textContent": "188", + "textContent": "42", "type": [ "PublicationXref", "PubMed:8968737" @@ -36078,7 +36078,7 @@ "id": "publicationXrefcc7", "source": "Nephrology (Carlton)", "standardName": "Review article: Coagulation cascade and therapeutics update: relevance to nephrology. Part 1: Overview of coagulation, thrombophilias and history of anticoagulants.", - "textContent": "160", + "textContent": "244", "type": [ "PublicationXref", "PubMed:19674315" @@ -36099,7 +36099,7 @@ "id": "publicationXrefcd0", "source": "Clin Rheumatol", "standardName": "A study on soluble intercellular adhesion molecule-1 and selenium in patients with rheumatoid arthritis complicated by vasculitis.", - "textContent": "294", + "textContent": "274", "type": [ "PublicationXref", "PubMed:14677018" @@ -36123,7 +36123,7 @@ "id": "publicationXrefcd2", "source": "Hepatology", "standardName": "Bile acid synthesis in primary cultures of rat and human hepatocytes.", - "textContent": "23", + "textContent": "48", "type": [ "PublicationXref", "PubMed:9462665" @@ -36140,7 +36140,7 @@ "id": "publicationXrefcd4", "source": "Semin Vasc Med", "standardName": "Homocysteine: overview of biochemistry, molecular biology, and role in disease processes.", - "textContent": "222", + "textContent": "116", "type": [ "PublicationXref", "PubMed:16047261" @@ -36158,7 +36158,7 @@ "id": "publicationXrefcd5", "source": "Mol Genet Metab", "standardName": "3beta-hydroxysterol Delta7-reductase and the Smith-Lemli-Opitz syndrome.", - "textContent": "132", + "textContent": "117", "type": [ "PublicationXref", "PubMed:15670717" @@ -36179,7 +36179,7 @@ "id": "publicationXrefcda", "source": "Eur J Clin Nutr", "standardName": "Effect of riboflavin supplementation on plasma homocysteine in elderly people with low riboflavin status.", - "textContent": "120", + "textContent": "273", "type": [ "PublicationXref", "PubMed:12209373" @@ -36196,7 +36196,7 @@ "id": "publicationXrefcdb", "source": "Diabetes", "standardName": "The biology of peroxisome proliferator-activated receptors: relationship with lipid metabolism and insulin sensitivity.", - "textContent": "48", + "textContent": "215", "type": [ "PublicationXref", "PubMed:14749265" @@ -36219,7 +36219,7 @@ "id": "publicationXrefce5", "source": "Eur J Biochem", "standardName": "Purification and characterization of a mutant human platelet phospholipase A2 expressed in Escherichia coli. Cleavage of a fusion protein with cyanogen bromide.", - "textContent": "269", + "textContent": "191", "type": [ "PublicationXref", "PubMed:1730245" @@ -36244,7 +36244,7 @@ "id": "publicationXrefce6", "source": "J Immunol", "standardName": "Inhibition of human neutrophil superoxide generation by alpha 1-antichymotrypsin.", - "textContent": "11", + "textContent": "299", "type": [ "PublicationXref", "PubMed:1848582" @@ -36261,7 +36261,7 @@ "id": "publicationXrefce8", "source": "Free Radic Res.", "standardName": "Isoprostanes: novel bioactive products of lipid peroxidation.", - "textContent": "49", + "textContent": "214", "type": [ "PublicationXref", "PubMed:15104204" @@ -36279,7 +36279,7 @@ "id": "publicationXrefceb", "source": "J Biol Chem", "standardName": "Nitric oxide is a physiological substrate for mammalian peroxidases.", - "textContent": "37", + "textContent": "62", "type": [ "PublicationXref", "PubMed:11090610" @@ -36300,7 +36300,7 @@ "id": "publicationXrefcef", "source": "Diabetes Metab Res Rev", "standardName": "Hemoglobin variants and determination of glycated hemoglobin (HbA1c).", - "textContent": "111", + "textContent": "203", "type": [ "PublicationXref", "PubMed:11307174" @@ -36317,7 +36317,7 @@ "id": "publicationXrefcf3", "source": "Annu Rev Nutr", "standardName": "Homocysteine metabolism.", - "textContent": "284", + "textContent": "61", "type": [ "PublicationXref", "PubMed:10448523" @@ -36335,7 +36335,7 @@ "id": "publicationXrefcf5", "source": "Biochim Biophys Acta", "standardName": "6alpha-hydroxylation of taurochenodeoxycholic acid and lithocholic acid by CYP3A4 in human liver microsomes.", - "textContent": "104", + "textContent": "60", "type": [ "PublicationXref", "PubMed:10216279" @@ -36354,7 +36354,7 @@ "id": "publicationXrefcf6", "source": "Proc Natl Acad Sci U S A", "standardName": "Interconversion of leukotrienes catalyzed by purified gamma-glutamyl transpeptidase: concomitant formation of leukotriene D4 and gamma-glutamyl amino acids.", - "textContent": "6", + "textContent": "13", "type": [ "PublicationXref", "PubMed:6122208" @@ -36372,7 +36372,7 @@ "id": "publicationXrefcf9", "source": "J Lipid Res", "standardName": "Absorption and lipoprotein transport of sphingomyelin.", - "textContent": "60", + "textContent": "126", "type": [ "PublicationXref", "PubMed:16251722" @@ -36395,7 +36395,7 @@ "id": "publicationXrefcfb", "source": "Pediatrics", "standardName": "Determinants of cobalamin status in newborns.", - "textContent": "288", + "textContent": "78", "type": [ "PublicationXref", "PubMed:11533328" @@ -36414,7 +36414,7 @@ "id": "publicationXrefcfc", "source": "Blood", "standardName": "Enzymic studies on phosphatidic acid synthesis in human platelets.", - "textContent": "1", + "textContent": "2", "type": [ "PublicationXref", "PubMed:4690137" @@ -36437,7 +36437,7 @@ "id": "publicationXrefd00", "source": "FASEB J", "standardName": "Cyclooxygenase in biology and disease.", - "textContent": "195", + "textContent": "197", "type": [ "PublicationXref", "PubMed:9737710" @@ -36459,7 +36459,7 @@ "id": "publicationXrefd08", "source": "Eur J Clin Pharmacol", "standardName": "The effects of folate supplementation on some coagulation parameters and oxidative status surrogates.", - "textContent": "41", + "textContent": "89", "type": [ "PublicationXref", "PubMed:11956665" @@ -36480,7 +36480,7 @@ "id": "publicationXrefd09", "source": "Nature", "standardName": "A membrane protein complex mediates retro-translocation from the ER lumen into the cytosol.", - "textContent": "216", + "textContent": "104", "type": [ "PublicationXref", "PubMed:15215856" @@ -36502,7 +36502,7 @@ "id": "publicationXrefd0b", "source": "Cell Mol Life Sci", "standardName": "Enzymology of NAD+ homeostasis in man.", - "textContent": "125", + "textContent": "277", "type": [ "PublicationXref", "PubMed:14704851" @@ -36520,7 +36520,7 @@ "id": "publicationXrefd18", "source": "Prostaglandins Other Lipid Mediat", "standardName": "Thromboxane synthase: structure and function of protein and gene.", - "textContent": "209", + "textContent": "210", "type": [ "PublicationXref", "PubMed:12432933" @@ -36543,7 +36543,7 @@ "id": "publicationXrefd29", "source": "Circulation", "standardName": "Relationships between homocysteine, factor VIIa, and thrombin generation in acute coronary syndromes.", - "textContent": "202", + "textContent": "63", "type": [ "PublicationXref", "PubMed:10653827" @@ -36584,7 +36584,7 @@ "id": "publicationXrefd34", "source": "J Clin Invest", "standardName": "Cyclic adenosine 3',5'-monophosphate inhibits the availability of arachidonate to prostaglandin synthetase in human platelet suspensions.", - "textContent": "86", + "textContent": "293", "type": [ "PublicationXref", "PubMed:190267" @@ -36610,7 +36610,7 @@ "id": "publicationXrefd42", "source": "Cytokine", "standardName": "Activation of the selenoprotein SEPS1 gene expression by pro-inflammatory cytokines in HepG2 cells.", - "textContent": "62", + "textContent": "128", "type": [ "PublicationXref", "PubMed:16574427" @@ -36627,7 +36627,7 @@ "id": "publicationXrefd4f", "source": "Am J Clin Nutr", "standardName": "Fatty acid metabolism in health and disease: the role of delta-6-desaturase.", - "textContent": "182", + "textContent": "301", "type": [ "PublicationXref", "PubMed:8386433" @@ -36650,7 +36650,7 @@ "id": "publicationXrefd53", "source": "J Cardiovasc Pharmacol", "standardName": "Roles of MAPK and NF-kappaB in interleukin-6 induction by lipopolysaccharide in vascular smooth muscle cells.", - "textContent": "70", + "textContent": "236", "type": [ "PublicationXref", "PubMed:18209571" @@ -36667,7 +36667,7 @@ "id": "publicationXrefd63", "source": "Mutat Res", "standardName": "Lipid peroxidation-DNA damage by malondialdehyde.", - "textContent": "29", + "textContent": "265", "type": [ "PublicationXref", "PubMed:10064852" @@ -36689,7 +36689,7 @@ "id": "publicationXrefd6f", "source": "Ann Neurol", "standardName": "Oxidative stress in SEPN1-related myopathy: from pathophysiology to treatment.", - "textContent": "321", + "textContent": "245", "type": [ "PublicationXref", "PubMed:19557870" @@ -36707,7 +36707,7 @@ "id": "publicationXrefd74", "source": "J Biol Chem", "standardName": "CTP: Phosphocholine cytidylyltransferase: paving the way from gene to membrane.", - "textContent": "221", + "textContent": "110", "type": [ "PublicationXref", "PubMed:15536089" @@ -36733,7 +36733,7 @@ "id": "publicationXrefd77", "source": "Nutr Metab Cardiovasc Dis", "standardName": "Associations of plasma homocysteine level with brachial-ankle pulse wave velocity, LDL atherogenicity, and inflammation profile in healthy men.", - "textContent": "329", + "textContent": "330", "type": [ "PublicationXref", "PubMed:19854035" @@ -36752,7 +36752,7 @@ "id": "publicationXrefd7f", "source": "Am J Clin Nutr", "standardName": "Studies of biomarker responses to intervention with vitamin B-12: a systematic review of randomized controlled trials.", - "textContent": "237", + "textContent": "248", "type": [ "PublicationXref", "PubMed:19403638" @@ -36779,7 +36779,7 @@ "id": "publicationXrefd82", "source": "J Nutr", "standardName": "Plasma S-adenosylhomocysteine is a better biomarker of atherosclerosis than homocysteine in apolipoprotein E-deficient mice fed high dietary methionine.", - "textContent": "314", + "textContent": "287", "type": [ "PublicationXref", "PubMed:18203897" @@ -36796,7 +36796,7 @@ "id": "publicationXrefd95", "source": "Prostaglandins", "standardName": "Lipoxins and novel aspirin-triggered 15-epi-lipoxins (ATL): a jungle of cell-cell interactions or a therapeutic opportunity?", - "textContent": "191", + "textContent": "195", "type": [ "PublicationXref", "PubMed:9112289" @@ -36817,7 +36817,7 @@ "id": "publicationXrefd97", "source": "Neurochem Int", "standardName": "Activity of phosphatidylethanolamine-N-methyltransferase in brain affected by Alzheimer's disease.", - "textContent": "283", + "textContent": "58", "type": [ "PublicationXref", "PubMed:10100195" @@ -36834,7 +36834,7 @@ "id": "publicationXrefd98", "source": "Gut", "standardName": "Studies on long chain fatty acid:CoA ligase from human small intestine.", - "textContent": "170", + "textContent": "294", "type": [ "PublicationXref", "PubMed:7429333" @@ -36859,7 +36859,7 @@ "id": "publicationXrefd99", "source": "J Biol Chem", "standardName": "Cloning of a novel human diacylglycerol kinase (DGKtheta) containing three cysteine-rich domains, a proline-rich region, and a pleckstrin homology domain with an overlapping Ras-associating domain.", - "textContent": "276", + "textContent": "260", "type": [ "PublicationXref", "PubMed:9099683" @@ -36880,7 +36880,7 @@ "id": "publicationXrefd9c", "source": "Proc Natl Acad Sci U S A", "standardName": "Triene prostaglandins: prostacyclin and thromboxane biosynthesis and unique biological properties.", - "textContent": "169", + "textContent": "6", "type": [ "PublicationXref", "PubMed:218223" @@ -36903,7 +36903,7 @@ "id": "publicationXrefda1", "source": "J Biol Chem", "standardName": "Plasma membrane rafts complete cholesterol synthesis by participating in retrograde movement of precursor sterols.", - "textContent": "69", + "textContent": "320", "type": [ "PublicationXref", "PubMed:17916561" @@ -36927,7 +36927,7 @@ "id": "publicationXrefda2", "source": "Atherosclerosis", "standardName": "Regulation of selenoprotein GPx4 expression and activity in human endothelial cells by fatty acids, cytokines and antioxidants.", - "textContent": "293", + "textContent": "213", "type": [ "PublicationXref", "PubMed:14642406" @@ -36952,7 +36952,7 @@ "id": "publicationXrefda3", "source": "J Exp Med", "standardName": "A type I interferon autocrine-paracrine loop is involved in Toll-like receptor-induced interleukin-12p70 secretion by dendritic cells.", - "textContent": "134", + "textContent": "111", "type": [ "PublicationXref", "PubMed:15851485" @@ -36969,7 +36969,7 @@ "id": "publicationXrefdab", "source": "Crit Rev Clin Lab Sci.", "standardName": "Vitamin B12 binders (transcobalamins) in serum.", - "textContent": "174", + "textContent": "16", "type": [ "PublicationXref", "PubMed:6295699" @@ -36989,7 +36989,7 @@ "id": "publicationXrefdac", "source": "J Lipid Res", "standardName": "Serine-palmitoyl transferase activity in cultured human keratinocytes.", - "textContent": "9", + "textContent": "258", "type": [ "PublicationXref", "PubMed:2246616" @@ -37014,7 +37014,7 @@ "id": "publicationXrefdb4", "source": "FEBS Lett", "standardName": "Purification, cDNA-cloning and expression of human diacylglycerol kinase.", - "textContent": "10", + "textContent": "190", "type": [ "PublicationXref", "PubMed:2175712" @@ -37042,7 +37042,7 @@ "id": "publicationXrefdb6", "source": "Clin Exp Allergy", "standardName": "Synthetic double-stranded RNA induces multiple genes related to inflammation through Toll-like receptor 3 depending on NF-kappaB and/or IRF-3 in airway epithelial cells.", - "textContent": "57", + "textContent": "118", "type": [ "PublicationXref", "PubMed:16911361" @@ -37062,7 +37062,7 @@ "id": "publicationXrefdb9", "source": "J Biol Chem", "standardName": "A new human selenium-containing protein. Purification, characterization, and cDNA sequence.", - "textContent": "197", + "textContent": "51", "type": [ "PublicationXref", "PubMed:9535873" @@ -37081,7 +37081,7 @@ "id": "publicationXrefdc8", "source": "Annu Rev Nutr.", "standardName": "Vitamin E, oxidative stress, and inflammation.", - "textContent": "127", + "textContent": "105", "type": [ "PublicationXref", "PubMed:16011463" @@ -37098,7 +37098,7 @@ "id": "publicationXrefdd0", "source": "Cell Mol Life Sci", "standardName": "Selenoprotein W: a review.", - "textContent": "36", + "textContent": "74", "type": [ "PublicationXref", "PubMed:11215511" @@ -37124,7 +37124,7 @@ "id": "publicationXrefdd2", "source": "Prostaglandins.", "standardName": "Synthesis and biological activities of leukotriene F4 and leukotriene F4 sulfone.", - "textContent": "172", + "textContent": "255", "type": [ "PublicationXref", "PubMed:6300970" @@ -37144,7 +37144,7 @@ "id": "publicationXrefdd8", "source": "Steroids", "standardName": "Homology modelling of human DHCR24 (seladin-1) and analysis of its binding properties through molecular docking and dynamics simulations.", - "textContent": "317", + "textContent": "286", "type": [ "PublicationXref", "PubMed:18394665" @@ -37166,7 +37166,7 @@ "id": "publicationXrefddc", "source": "Hippocampus", "standardName": "Pyridoxine 5'-phosphate oxidase, not pyridoxal kinase, involves in long-term potentiation induction in the rat dentate gyrus.", - "textContent": "320", + "textContent": "242", "type": [ "PublicationXref", "PubMed:18680158" @@ -37185,7 +37185,7 @@ "id": "publicationXrefdde", "source": "Mol Cell Biol", "standardName": "Regulation of tumor necrosis factor alpha transcription in macrophages: involvement of four kappa B-like motifs and of constitutive and inducible forms of NF-kappa B.", - "textContent": "91", + "textContent": "175", "type": [ "PublicationXref", "PubMed:2181276" @@ -37204,7 +37204,7 @@ "id": "publicationXrefde0", "source": "Antioxid Redox Signal", "standardName": "Evolution of catalases from bacteria to humans.", - "textContent": "149", + "textContent": "234", "type": [ "PublicationXref", "PubMed:18498226" @@ -37226,7 +37226,7 @@ "id": "publicationXrefde8", "source": "Biochem Soc Trans", "standardName": "Removal of triacylglycerols from chylomicrons and VLDL by capillary beds: the basis of lipoprotein remnant formation.", - "textContent": "231", + "textContent": "229", "type": [ "PublicationXref", "PubMed:17511631" @@ -37245,7 +37245,7 @@ "id": "publicationXrefdf7", "source": "Anal Biochem", "standardName": "Radioassay of bile acid coenzyme A:glycine/taurine: N-acyltransferase using an n-butanol solvent extraction procedure.", - "textContent": "179", + "textContent": "24", "type": [ "PublicationXref", "PubMed:2610352" @@ -37265,7 +37265,7 @@ "id": "publicationXrefe06", "source": "J Am Coll Nutr", "standardName": "Anxiety and adipose essential fatty acid precursors for prostaglandin E1 and E2.", - "textContent": "281", + "textContent": "263", "type": [ "PublicationXref", "PubMed:9627909" @@ -37283,7 +37283,7 @@ "id": "publicationXrefe0b", "source": "J Clin Invest", "standardName": "Deiodinases: implications of the local control of thyroid hormone action.", - "textContent": "138", + "textContent": "280", "type": [ "PublicationXref", "PubMed:17016550" @@ -37313,7 +37313,7 @@ "id": "publicationXrefe0e", "source": "Clin Cardiol", "standardName": "Associations between C-reactive protein and circulating cell adhesion molecules in patients with unstable angina undergoing coronary intervention and their clinical implication.", - "textContent": "130", + "textContent": "221", "type": [ "PublicationXref", "PubMed:15704532" @@ -37341,7 +37341,7 @@ "id": "publicationXrefe0f", "source": "Circ Res", "standardName": "Imbalance between xanthine oxidase and nitric oxide synthase signaling pathways underlies mechanoenergetic uncoupling in the failing heart.", - "textContent": "205", + "textContent": "83", "type": [ "PublicationXref", "PubMed:11861418" @@ -37365,7 +37365,7 @@ "id": "publicationXrefe10", "source": "J Neurochem", "standardName": "Human S-adenosylhomocysteine hydrolase: common gene sequence variation and functional genomic characterization.", - "textContent": "156", + "textContent": "154", "type": [ "PublicationXref", "PubMed:19619139" @@ -37385,7 +37385,7 @@ "id": "publicationXrefe11", "source": "J Trace Elem Med Biol", "standardName": "Selenium status and its correlates in a British national diet and nutrition survey: people aged 65 years and over.", - "textContent": "116", + "textContent": "90", "type": [ "PublicationXref", "PubMed:11878747" @@ -37405,7 +37405,7 @@ "id": "publicationXrefe14", "source": "J Biol Chem", "standardName": "Membrane topography of human phosphatidylethanolamine N-methyltransferase.", - "textContent": "215", + "textContent": "92", "type": [ "PublicationXref", "PubMed:12431977" @@ -37425,7 +37425,7 @@ "id": "publicationXrefe15", "source": "Arch Biochem Biophys", "standardName": "Human isopentenyl diphosphate: dimethylallyl diphosphate isomerase: overproduction, purification, and characterization.", - "textContent": "187", + "textContent": "41", "type": [ "PublicationXref", "PubMed:8806705" @@ -37450,7 +37450,7 @@ "id": "publicationXrefe18", "source": "FEBS Lett", "standardName": "Functional characterization of human sphingosine kinase-1.", - "textContent": "285", + "textContent": "66", "type": [ "PublicationXref", "PubMed:10802064" @@ -37468,7 +37468,7 @@ "id": "publicationXrefe1b", "source": "J Invest Dermatol", "standardName": "Sphingomyelinase in pig and human epidermis.", - "textContent": "2", + "textContent": "4", "type": [ "PublicationXref", "PubMed:25935" @@ -37488,7 +37488,7 @@ "id": "publicationXrefe1e", "source": "Biochem Biophys Res Commun", "standardName": "Molecular cloning of the human gene encoding lanosterol synthase from a liver cDNA library.", - "textContent": "185", + "textContent": "259", "type": [ "PublicationXref", "PubMed:7639730" @@ -37511,7 +37511,7 @@ "id": "publicationXrefe26", "source": "J Biol Chem", "standardName": "Reactive oxygen species-induced phosphorylation of p53 on serine 20 is mediated in part by polo-like kinase-3.", - "textContent": "204", + "textContent": "307", "type": [ "PublicationXref", "PubMed:11447225" @@ -37531,7 +37531,7 @@ "id": "publicationXrefe2b", "source": "Cell Immunol", "standardName": "Synergism of Toll-like receptor-induced interleukin-12p70 secretion by monocyte-derived dendritic cells is mediated through p38 MAPK and lowers the threshold of T-helper cell type 1 responses.", - "textContent": "309", + "textContent": "130", "type": [ "PublicationXref", "PubMed:17927969" @@ -37549,7 +37549,7 @@ "id": "publicationXrefe2c", "source": "Biochim Biophys Acta", "standardName": "Expression and characterization of human group V phospholipase A2.", - "textContent": "103", + "textContent": "56", "type": [ "PublicationXref", "PubMed:9767110" @@ -37568,7 +37568,7 @@ "id": "publicationXrefe2d", "source": "Biofactors", "standardName": "The influence of the cytokines Il-1beta and INFgamma on the expression of selenoproteins in the human hepatocarcinoma cell line HepG2.", - "textContent": "34", + "textContent": "270", "type": [ "PublicationXref", "PubMed:10705969" @@ -37593,7 +37593,7 @@ "id": "publicationXrefe2f", "source": "Cancer Res", "standardName": "Folate receptor beta is expressed by tumor-associated macrophages and constitutes a marker for M2 anti-inflammatory/regulatory macrophages.", - "textContent": "319", + "textContent": "153", "type": [ "PublicationXref", "PubMed:19951991" @@ -37610,7 +37610,7 @@ "id": "publicationXrefe34", "source": "Biomed Pharmacother", "standardName": "The serum levels of soluble intercellular adhesion molecule-1 (sICAM-1) and soluble gp130 (sgp130) in different tumour stages. Correlation between the two parameters in progression of malignancy.", - "textContent": "133", + "textContent": "319", "type": [ "PublicationXref", "PubMed:16202558" @@ -37636,7 +37636,7 @@ "id": "publicationXrefe37", "source": "Blood", "standardName": "Interferon regulatory factor 3 is involved in Toll-like receptor 4 (TLR4)- and TLR3-induced IL-12p35 gene activation.", - "textContent": "136", + "textContent": "122", "type": [ "PublicationXref", "PubMed:16219795" @@ -37655,7 +37655,7 @@ "id": "publicationXrefe3f", "source": "Immunobiology", "standardName": "Tumor necrosis factor-alpha up-regulates the expression of CCL2 and adhesion molecules of human proximal tubular epithelial cells through MAPK signaling pathways.", - "textContent": "148", + "textContent": "141", "type": [ "PublicationXref", "PubMed:18656701" @@ -37675,7 +37675,7 @@ "id": "publicationXrefe44", "source": "J Biol Chem", "standardName": "Leukotriene E4 elimination and metabolism in normal human subjects.", - "textContent": "266", + "textContent": "25", "type": [ "PublicationXref", "PubMed:2174886" @@ -37695,7 +37695,7 @@ "id": "publicationXrefe4c", "source": "J Biol Chem", "standardName": "Overexpression of a mammalian ethanolamine-specific kinase accelerates the CDP-ethanolamine pathway.", - "textContent": "38", + "textContent": "204", "type": [ "PublicationXref", "PubMed:11044454" @@ -37713,7 +37713,7 @@ "id": "publicationXrefe4d", "source": "J Nutr", "standardName": "Folate and carcinogenesis: an integrated scheme.", - "textContent": "35", + "textContent": "64", "type": [ "PublicationXref", "PubMed:10720158" @@ -37737,7 +37737,7 @@ "id": "publicationXrefe51", "source": "J Clin Endocrinol Metab", "standardName": "Molecular genetics of 3beta-hydroxy-Delta5-C27-steroid oxidoreductase deficiency in 16 patients with loss of bile acid synthesis and liver disease.", - "textContent": "214", + "textContent": "276", "type": [ "PublicationXref", "PubMed:12679481" @@ -37755,7 +37755,7 @@ "id": "publicationXrefe58", "source": "Eur J Dermatol", "standardName": "The Conradi-Hünermann-Happle syndrome is caused by mutations in the gene that encodes a 8- 7 sterol isomerase and is biochemically related to the CHILD syndrome.", - "textContent": "287", + "textContent": "75", "type": [ "PublicationXref", "PubMed:10980461" @@ -37774,7 +37774,7 @@ "id": "publicationXrefe64", "source": "Eur J Biochem", "standardName": "Acyl-donor specificities of partially purified 1-acylglycerophosphate acyltransferase, 2-acylglycerophosphate acyltransferase and 1-acylglycerophosphorylcholine acyltransferase from rat-liver microsomes.", - "textContent": "251", + "textContent": "292", "type": [ "PublicationXref", "PubMed:4774123" @@ -37794,7 +37794,7 @@ "id": "publicationXrefe66", "source": "Trends Mol Med", "standardName": "Insulin resistance and oxidative stress interdependency in non-alcoholic fatty liver disease.", - "textContent": "135", + "textContent": "227", "type": [ "PublicationXref", "PubMed:17049925" @@ -37814,7 +37814,7 @@ "id": "publicationXrefe68", "source": "J Lipid Res", "standardName": "Conversion of linoleic acid into arachidonic acid by cultured murine and human keratinocytes.", - "textContent": "177", + "textContent": "188", "type": [ "PublicationXref", "PubMed:2448410" @@ -37835,7 +37835,7 @@ "id": "publicationXrefe70", "source": "Biochemistry", "standardName": "Human glycinamide ribonucleotide transformylase: active site mutants as mechanistic probes.", - "textContent": "146", + "textContent": "131", "type": [ "PublicationXref", "PubMed:17198385" @@ -37852,7 +37852,7 @@ "id": "publicationXrefe71", "source": "Annu Rev Biochem", "standardName": "Leukotrienes.", - "textContent": "260", + "textContent": "18", "type": [ "PublicationXref", "PubMed:6311078" @@ -37873,7 +37873,7 @@ "id": "publicationXrefe72", "source": "J Immunol", "standardName": "1-Methyl-tryptophan can interfere with TLR signaling in dendritic cells independently of IDO activity.", - "textContent": "142", + "textContent": "228", "type": [ "PublicationXref", "PubMed:16887964" @@ -37901,7 +37901,7 @@ "id": "publicationXrefe73", "source": "J Med Virol", "standardName": "Impaired cytokine response in myeloid dendritic cells in chronic hepatitis C virus infection regardless of enhanced expression of Toll-like receptors and retinoic acid inducible gene-I.", - "textContent": "151", + "textContent": "239", "type": [ "PublicationXref", "PubMed:18428149" @@ -37923,7 +37923,7 @@ "id": "publicationXrefe74", "source": "J Biol Chem", "standardName": "Role of human sphingosine-1-phosphate phosphatase 1 in the regulation of intra- and extracellular sphingosine-1-phosphate levels and cell viability.", - "textContent": "47", + "textContent": "94", "type": [ "PublicationXref", "PubMed:12815058" @@ -37943,7 +37943,7 @@ "id": "publicationXrefe78", "source": "J Biol Chem", "standardName": "Purification and characterization of UDP-glucose:ceramide glucosyltransferase from rat liver Golgi membranes.", - "textContent": "274", + "textContent": "40", "type": [ "PublicationXref", "PubMed:8567691" @@ -37961,7 +37961,7 @@ "id": "publicationXrefe7f", "source": "Pharm World Sci", "standardName": "Pharmacological inhibition of leukotriene actions.", - "textContent": "21", + "textContent": "50", "type": [ "PublicationXref", "PubMed:9584338" @@ -37978,7 +37978,7 @@ "id": "publicationXrefe80", "source": "Linus Paulin institute", "standardName": "Vitamin B 6", - "textContent": "161", + "textContent": "316", "type": [ "PublicationXref" ], @@ -37994,7 +37994,7 @@ "id": "publicationXrefe85", "source": "Prog Lipid Res", "standardName": "Fatty acid elongases in mammals: their regulation and roles in metabolism.", - "textContent": "137", + "textContent": "281", "type": [ "PublicationXref", "PubMed:16564093" @@ -38019,7 +38019,7 @@ "id": "publicationXrefe88", "source": "J Lipid Res", "standardName": "Formation and antiproliferative effect of prostaglandin E(3) from eicosapentaenoic acid in human lung cancer cells.", - "textContent": "217", + "textContent": "100", "type": [ "PublicationXref", "PubMed:14993240" @@ -38037,7 +38037,7 @@ "id": "publicationXrefe99", "source": "Circ Res", "standardName": "New insights into the regulation of HDL metabolism and reverse cholesterol transport.", - "textContent": "298", + "textContent": "108", "type": [ "PublicationXref", "PubMed:15976321" @@ -38055,7 +38055,7 @@ "id": "publicationXrefe9b", "source": "Bioessays", "standardName": "Inflammation, antichymotrypsin, and lipid metabolism: autogenic etiology of Alzheimer's disease.", - "textContent": "280", + "textContent": "52", "type": [ "PublicationXref", "PubMed:10048303" @@ -38074,7 +38074,7 @@ "id": "publicationXrefea2", "source": "J Lipid Res", "standardName": "Effects of serum amyloid A protein (SAA) on composition, size, and density of high density lipoproteins in subjects with myocardial infarction.", - "textContent": "176", + "textContent": "187", "type": [ "PublicationXref", "PubMed:4086942" @@ -38086,7 +38086,7 @@ "publicationXrefea3": { "gpmlElementName": "PublicationXref", "id": "publicationXrefea3", - "textContent": "249", + "textContent": "315", "type": [ "PublicationXref" ], @@ -38103,7 +38103,7 @@ "id": "publicationXrefeac", "source": "Steroids", "standardName": "Lathosterol side chain amides: a new class of human lathosterol oxidase inhibitors.", - "textContent": "234", + "textContent": "314", "type": [ "PublicationXref", "PubMed:18164739" @@ -38122,7 +38122,7 @@ "id": "publicationXrefeb5", "source": "Pharmacol Rev", "standardName": "Cyclooxygenase isozymes: the biology of prostaglandin synthesis and inhibition.", - "textContent": "126", + "textContent": "97", "type": [ "PublicationXref", "PubMed:15317910" @@ -38142,7 +38142,7 @@ "id": "publicationXrefeb6", "source": "Prostaglandins Other Lipid Mediat", "standardName": "Prostaglandin E synthase.", - "textContent": "117", + "textContent": "272", "type": [ "PublicationXref", "PubMed:12432931" @@ -38185,7 +38185,7 @@ "id": "publicationXrefebc", "source": "J Biol Chem", "standardName": "Involvement of dihydroceramide desaturase in cell cycle progression in human neuroblastoma cells.", - "textContent": "310", + "textContent": "133", "type": [ "PublicationXref", "PubMed:17283068" @@ -38209,7 +38209,7 @@ "id": "publicationXrefebf", "source": "J Leukoc Biol", "standardName": "NF-{kappa}B is required for STAT-4 expression during dendritic cell maturation.", - "textContent": "232", + "textContent": "129", "type": [ "PublicationXref", "PubMed:17046972" @@ -38226,7 +38226,7 @@ "id": "publicationXrefec3", "source": "http://www.wikipathways.org/index.php/Pathway:Homo_sapiens:Selenoproteins", "standardName": "Selenoproteins", - "textContent": "164", + "textContent": "291", "type": [ "PublicationXref" ], @@ -38241,7 +38241,7 @@ "id": "publicationXrefec4", "source": "Biochem Pharmacol", "standardName": "The controversial place of vitamin C in cancer treatment.", - "textContent": "72", + "textContent": "324", "type": [ "PublicationXref", "PubMed:18938145" @@ -38264,7 +38264,7 @@ "id": "publicationXrefecb", "source": "Mol Cell Endocrinol", "standardName": "Structure-activity relationships of human AKR-type oxidoreductases involved in bile acid synthesis: AKR1D1 and AKR1C4.", - "textContent": "318", + "textContent": "143", "type": [ "PublicationXref", "PubMed:19013211" @@ -38281,7 +38281,7 @@ "id": "publicationXrefed1", "source": "Adv Clin Chem", "standardName": "Proinflammatory cytokines in CRP baseline regulation.", - "textContent": "240", + "textContent": "328", "type": [ "PublicationXref", "PubMed:19803417" @@ -38305,7 +38305,7 @@ "id": "publicationXrefed4", "source": "J Biol Chem", "standardName": "Necessary role for the Lag1p motif in (dihydro)ceramide synthase activity.", - "textContent": "58", + "textContent": "119", "type": [ "PublicationXref", "PubMed:16951403" @@ -38324,7 +38324,7 @@ "id": "publicationXrefed6", "source": "J Clin Invest", "standardName": "Selective release of archidonic acid from the phospholipids of human platelets in response to thrombin.", - "textContent": "254", + "textContent": "3", "type": [ "PublicationXref", "PubMed:874074" @@ -38341,7 +38341,7 @@ "id": "publicationXrefed9", "source": "Annu Rev Nutr", "standardName": "Vitamin E: interactions with free radicals and ascorbate.", - "textContent": "88", + "textContent": "297", "type": [ "PublicationXref", "PubMed:2992548" @@ -38359,7 +38359,7 @@ "id": "publicationXrefedb", "source": "Methods Enzymol", "standardName": "Measurement of ceramide synthase activity.", - "textContent": "32", + "textContent": "269", "type": [ "PublicationXref", "PubMed:10914032" @@ -38379,7 +38379,7 @@ "id": "publicationXrefee3", "source": "J Biol Chem", "standardName": "Sphingolipid base metabolism. Stereospecific uptake of proton in the enzymatic conversion of sphinganine 1-phosphate to ethanolamine 1-phosphate.", - "textContent": "253", + "textContent": "171", "type": [ "PublicationXref", "PubMed:932041" @@ -38397,7 +38397,7 @@ "id": "publicationXrefee5", "source": "Biochim Biophys Acta", "standardName": "UDPgalactose:glucosylceramide beta 1----4-galactosyltransferase activity in human proximal tubular cells from normal and familial hypercholesterolemic homozygotes.", - "textContent": "8", + "textContent": "22", "type": [ "PublicationXref", "PubMed:3099851" @@ -38420,7 +38420,7 @@ "id": "publicationXrefeec", "source": "Antioxid Redox Signal", "standardName": "GPx2 counteracts PGE2 production by dampening COX-2 and mPGES-1 expression in human colon cancer cells.", - "textContent": "312", + "textContent": "139", "type": [ "PublicationXref", "PubMed:18479189" @@ -38440,7 +38440,7 @@ "id": "publicationXrefeed", "source": "J Lipid Res", "standardName": "Characterization of 11-HETE and 15-HETE, together with prostacyclin, as major products of the cyclooxygenase pathway in cultured rat aorta smooth muscle cells.", - "textContent": "261", + "textContent": "296", "type": [ "PublicationXref", "PubMed:6418841" @@ -38463,7 +38463,7 @@ "id": "publicationXrefef2", "source": "J Biol Chem", "standardName": "Identification of amino acids required for the functional up-regulation of human dihydrofolate reductase protein in response to antifolate Treatment.", - "textContent": "55", + "textContent": "220", "type": [ "PublicationXref", "PubMed:15817466" @@ -38483,7 +38483,7 @@ "id": "publicationXrefef6", "source": "Biochim Biophys Acta", "standardName": "Isolation and characterization of the human liver ethanolamine kinase.", - "textContent": "181", + "textContent": "298", "type": [ "PublicationXref", "PubMed:2167130" @@ -38505,7 +38505,7 @@ "id": "publicationXrefef8", "source": "Mol Pharmacol", "standardName": "The proton-coupled folate transporter: impact on pemetrexed transport and on antifolates activities compared with the reduced folate carrier.", - "textContent": "78", + "textContent": "144", "type": [ "PublicationXref", "PubMed:18524888" @@ -38527,7 +38527,7 @@ "id": "publicationXrefefa", "source": "J Lipid Res", "standardName": "Cofactor requiremets for 7 alpha-dehydroxylation of cholic and chenodeoxycholic acid in cell extracts of the intestinal anaerobic bacterium, Eubacterium species V.P.I. 13708.", - "textContent": "4", + "textContent": "12", "type": [ "PublicationXref", "PubMed:7276750" @@ -38554,7 +38554,7 @@ "id": "publicationXrefefb", "source": "Clin Immunol", "standardName": "Folate/homocysteine phenotypes and MTHFR 677C>T genotypes are associated with serum levels of monocyte chemoattractant protein-1.", - "textContent": "323", + "textContent": "161", "type": [ "PublicationXref", "PubMed:19625220" @@ -38573,7 +38573,7 @@ "id": "publicationXreff03", "source": "Pharmacol Ther", "standardName": "Cyclooxygenase and prostaglandin synthases in atherosclerosis: recent insights and future perspectives.", - "textContent": "152", + "textContent": "325", "type": [ "PublicationXref", "PubMed:18420277" @@ -38593,7 +38593,7 @@ "id": "publicationXreff11", "source": "J Proteome Res", "standardName": "Protein tyrosine nitration: selectivity, physicochemical and biological consequences, denitration, and proteomics methods for the identification of tyrosine-nitrated proteins.", - "textContent": "245", + "textContent": "249", "type": [ "PublicationXref", "PubMed:19415921" @@ -38610,7 +38610,7 @@ "id": "publicationXreff15", "source": "Free Radic Biol Med.", "standardName": "Free radicals, uric acid, and human disease.", - "textContent": "17", + "textContent": "39", "type": [ "PublicationXref", "PubMed:8846925" @@ -38627,7 +38627,7 @@ "id": "publicationXreff17", "source": "Adv Protein Chem", "standardName": "Fibrinogen and fibrin.", - "textContent": "224", + "textContent": "279", "type": [ "PublicationXref", "PubMed:15837518" @@ -38651,7 +38651,7 @@ "id": "publicationXreff18", "source": "J Biol Chem", "standardName": "15-deoxy-Delta(12,14)-prostaglandin J2 induces vascular endothelial cell apoptosis through the sequential activation of MAPKS and p53.", - "textContent": "74", + "textContent": "240", "type": [ "PublicationXref", "PubMed:18718914" @@ -38668,7 +38668,7 @@ "id": "publicationXreff1b", "source": "Annu Rev Nutr.", "standardName": "Homocysteine metabolism.", - "textContent": "105", + "textContent": "201", "type": [ "PublicationXref", "PubMed:10448523" @@ -38688,7 +38688,7 @@ "id": "publicationXreff1c", "source": "Trends Mol Med", "standardName": "p53 and the regulation of hepatocyte apoptosis: implications for disease pathogenesis.", - "textContent": "326", + "textContent": "159", "type": [ "PublicationXref", "PubMed:19822456" @@ -38707,7 +38707,7 @@ "id": "publicationXreff1e", "source": "J Nutr", "standardName": "Selenoprotein metabolism and function: evidence for more than one function for selenoprotein P.", - "textContent": "213", + "textContent": "317", "type": [ "PublicationXref", "PubMed:12730456" @@ -38725,7 +38725,7 @@ "id": "publicationXreff1f", "source": "Annu Rev Pharmacol Toxicol", "standardName": "Properties and biological activities of thioredoxins.", - "textContent": "112", + "textContent": "81", "type": [ "PublicationXref", "PubMed:11264458" @@ -38743,7 +38743,7 @@ "id": "publicationXreff21", "source": "Blood", "standardName": "Inhibition of thromboxane formation in vivo and ex vivo: implications for therapy with platelet inhibitory drugs.", - "textContent": "264", + "textContent": "257", "type": [ "PublicationXref", "PubMed:3790723" @@ -38764,7 +38764,7 @@ "id": "publicationXreff2b", "source": "J Lipid Res", "standardName": "Hepatic cholesterol metabolism in normo- and hyperlipidemic patients with cholesterol gallstones.", - "textContent": "256", + "textContent": "172", "type": [ "PublicationXref", "PubMed:374662" @@ -38783,7 +38783,7 @@ "id": "publicationXreff2d", "source": "DNA Cell Biol", "standardName": "Molecular cloning of two alternatively spliced forms of human phosphatidic acid phosphatase cDNAs that are differentially expressed in normal and tumor cells.", - "textContent": "192", + "textContent": "196", "type": [ "PublicationXref", "PubMed:9570154" @@ -38801,7 +38801,7 @@ "id": "publicationXreff38", "source": "Clin Rheumatol", "standardName": "The interrelation of glutathione reductase, catalase, glutathione peroxidase, superoxide dismutase, and glucose-6-phosphate in the pathogenesis of rheumatoid arthritis.", - "textContent": "80", + "textContent": "237", "type": [ "PublicationXref", "PubMed:17912575" @@ -38825,7 +38825,7 @@ "id": "publicationXreff3f", "source": "Proc Natl Acad Sci U S A", "standardName": "Cell proliferation and survival induced by Toll-like receptors is antagonized by type I IFNs.", - "textContent": "145", + "textContent": "283", "type": [ "PublicationXref", "PubMed:17463087" @@ -38850,7 +38850,7 @@ "id": "publicationXreff43", "source": "FEBS Lett", "standardName": "5-lipoxygenase-activating protein is an arachidonate binding protein.", - "textContent": "14", + "textContent": "302", "type": [ "PublicationXref", "PubMed:8440384" @@ -38867,7 +38867,7 @@ "id": "publicationXreff4a", "source": "Free Radic Biol Med", "standardName": "Tissue-specific functions of individual glutathione peroxidases.", - "textContent": "27", + "textContent": "182", "type": [ "PublicationXref", "PubMed:10569628" @@ -38886,7 +38886,7 @@ "id": "publicationXreff4c", "source": "IUBMB Life", "standardName": "The Sep15 protein family: roles in disulfide bond formation and quality control in the endoplasmic reticulum.", - "textContent": "68", + "textContent": "138", "type": [ "PublicationXref", "PubMed:17365173" @@ -38903,7 +38903,7 @@ "id": "publicationXreff4e", "source": "Free Radic Biol Med", "standardName": "Towards the physiological function of uric acid.", - "textContent": "95", + "textContent": "33", "type": [ "PublicationXref", "PubMed:8325534" @@ -38920,7 +38920,7 @@ "id": "publicationXreff4f", "source": "Biochim Biophys Acta", "standardName": "Phosphatidylserine decarboxylase.", - "textContent": "98", + "textContent": "194", "type": [ "PublicationXref", "PubMed:9370338" @@ -38941,7 +38941,7 @@ "id": "publicationXreff54", "source": "J Biol Chem", "standardName": "cDNA cloning of mouse and human cholesterol 25-hydroxylases, polytopic membrane proteins that synthesize a potent oxysterol regulator of lipid metabolism.", - "textContent": "101", + "textContent": "57", "type": [ "PublicationXref", "PubMed:9852097" @@ -38963,7 +38963,7 @@ "id": "publicationXreff5b", "source": "J Gastroenterol", "standardName": "Relationship of plasma folic acid and status of DNA methylation in human gastric cancer.", - "textContent": "100", + "textContent": "44", "type": [ "PublicationXref", "PubMed:9085163" @@ -38983,7 +38983,7 @@ "id": "publicationXreff5c", "source": "Immunol Lett", "standardName": "Inhibition of type 2,5'-deiodinase by tumor necrosis factor alpha, interleukin-6 and interferon gamma in human thyroid tissue.", - "textContent": "210", + "textContent": "85", "type": [ "PublicationXref", "PubMed:11716958" @@ -39001,7 +39001,7 @@ "id": "publicationXreff5d", "source": "Annu Rev Nutr", "standardName": "Structure, function, and dietary regulation of delta6, delta5, and delta9 desaturases.", - "textContent": "51", + "textContent": "99", "type": [ "PublicationXref", "PubMed:15189125" @@ -39019,7 +39019,7 @@ "id": "publicationXreff5f", "source": "Prostaglandins Leukot Essent Fatty Acids", "standardName": "5-lipoxygenase and FLAP.", - "textContent": "291", + "textContent": "309", "type": [ "PublicationXref", "PubMed:12895592" @@ -39040,7 +39040,7 @@ "id": "publicationXreff6c", "source": "Biochem J", "standardName": "The role of alpha-methylacyl-CoA racemase in bile acid synthesis.", - "textContent": "45", + "textContent": "84", "type": [ "PublicationXref", "PubMed:11964182" @@ -39061,7 +39061,7 @@ "id": "publicationXreff70", "source": "J Lipid Res", "standardName": "Docosahexaenoic acid synthesis in human skin fibroblasts involves peroxisomal retroconversion of tetracosahexaenoic acid.", - "textContent": "186", + "textContent": "35", "type": [ "PublicationXref", "PubMed:8656081" @@ -39078,7 +39078,7 @@ "id": "publicationXreff7a", "source": "Ann N Y Acad Sci", "standardName": "Elements of the fibrinolytic system.", - "textContent": "290", + "textContent": "205", "type": [ "PublicationXref", "PubMed:11460480" @@ -39099,7 +39099,7 @@ "id": "publicationXreff7b", "source": "Proc Natl Acad Sci U S A", "standardName": "Triene prostaglandins: prostaglandin D3 and icosapentaenoic acid as potential antithrombotic substances.", - "textContent": "166", + "textContent": "7", "type": [ "PublicationXref", "PubMed:230492" @@ -39119,7 +39119,7 @@ "id": "publicationXreff7c", "source": "J Interferon Cytokine Res", "standardName": "Repression of interleukin-2 and interleukin-4 promoters by tumor suppressor protein p53.", - "textContent": "16", + "textContent": "36", "type": [ "PublicationXref", "PubMed:8877730" @@ -39143,7 +39143,7 @@ "id": "publicationXreff7d", "source": "Eur J Immunol", "standardName": "Inhibition of phosphoinositide 3-kinase enhances TRIF-dependent NF-kappa B activation and IFN-beta synthesis downstream of Toll-like receptor 3 and 4.", - "textContent": "131", + "textContent": "311", "type": [ "PublicationXref", "PubMed:15940673" @@ -39167,7 +39167,7 @@ "id": "publicationXreff82", "source": "EMBO J", "standardName": "Toll-like receptor 3 associates with c-Src tyrosine kinase on endosomes to initiate antiviral signaling.", - "textContent": "61", + "textContent": "125", "type": [ "PublicationXref", "PubMed:16858407" @@ -39191,7 +39191,7 @@ "id": "publicationXreff84", "source": "Arterioscler Thromb Vasc Biol", "standardName": "Peroxidase properties of extracellular superoxide dismutase: role of uric acid in modulating in vivo activity.", - "textContent": "119", + "textContent": "206", "type": [ "PublicationXref", "PubMed:12231557" @@ -39209,7 +39209,7 @@ "id": "publicationXreff8c", "source": "J Clin Invest", "standardName": "Why there are two cyclooxygenase isozymes.", - "textContent": "115", + "textContent": "79", "type": [ "PublicationXref", "PubMed:11413152" @@ -39229,7 +39229,7 @@ "id": "publicationXreff8d", "source": "J Am Coll Cardiol", "standardName": "Omega-3 polyunsaturated fatty acids and cardiovascular diseases.", - "textContent": "159", + "textContent": "246", "type": [ "PublicationXref", "PubMed:19660687" @@ -39247,7 +39247,7 @@ "id": "publicationXreff92", "source": "Drug Metab Dispos", "standardName": "Identification of human hepatic cytochrome p450 enzymes involved in the biotransformation of cholic and chenodeoxycholic acid.", - "textContent": "73", + "textContent": "288", "type": [ "PublicationXref", "PubMed:18583509" @@ -39264,7 +39264,7 @@ "id": "publicationXreff96", "source": "Ingenuity software", "standardName": "Prostaglandin and Leukotriene Metabolism", - "textContent": "248", + "textContent": "165", "type": [ "PublicationXref" ], @@ -39281,7 +39281,7 @@ "id": "publicationXreff97", "source": "J Biol Chem", "standardName": "Reduction of dehydroascorbate to ascorbate by the selenoenzyme thioredoxin reductase.", - "textContent": "20", + "textContent": "43", "type": [ "PublicationXref", "PubMed:9278416" @@ -39302,7 +39302,7 @@ "id": "publicationXreff9c", "source": "J Biochem", "standardName": "Purification and characterization of rat sterol 14-demethylase P450 (CYP51) expressed in Escherichia coli.", - "textContent": "25", + "textContent": "305", "type": [ "PublicationXref", "PubMed:10544287" @@ -39322,7 +39322,7 @@ "id": "publicationXreffa0", "source": "EMBO J", "standardName": "Regulation of p53 tumour suppressor target gene expression by the p52 NF-kappaB subunit.", - "textContent": "301", + "textContent": "121", "type": [ "PublicationXref", "PubMed:16990795" @@ -39342,7 +39342,7 @@ "id": "publicationXreffad", "source": "Mol Pharmacol", "standardName": "Transformation of 5-hydroperoxyeicosatetraenoic acid into dihydroxy- and cysteinyl-leukotrienes by rat hepatocytes: effects of glutathione.", - "textContent": "92", + "textContent": "27", "type": [ "PublicationXref", "PubMed:1848655" @@ -39367,7 +39367,7 @@ "id": "publicationXreffb2", "source": "J Biol Chem", "standardName": "NMR structures of the selenoproteins Sep15 and SelM reveal redox activity of a new thioredoxin-like family.", - "textContent": "304", + "textContent": "312", "type": [ "PublicationXref", "PubMed:16319061" @@ -39390,7 +39390,7 @@ "id": "publicationXreffb3", "source": "Am J Physiol", "standardName": "Age-associated increase in PGE2 synthesis and COX activity in murine macrophages is reversed by vitamin E.", - "textContent": "102", + "textContent": "53", "type": [ "PublicationXref", "PubMed:9730949" @@ -39413,7 +39413,7 @@ "id": "publicationXreffb5", "source": "Am J Kidney Dis", "standardName": "Vitamin E suppresses 5-lipoxygenase-mediated oxidative stress in peripheral blood mononuclear cells of hemodialysis patients regardless of administration route.", - "textContent": "113", + "textContent": "77", "type": [ "PublicationXref", "PubMed:11325678" @@ -39434,7 +39434,7 @@ "id": "publicationXreffb6", "source": "FEBS Lett", "standardName": "Selenoprotein W is a glutathione-dependent antioxidant in vivo.", - "textContent": "121", + "textContent": "308", "type": [ "PublicationXref", "PubMed:12062442" @@ -39452,7 +39452,7 @@ "id": "publicationXreffb8", "source": "J Exp Med", "standardName": "Generation of unique mono-hydroxy-eicosatetraenoic acids from arachidonic acid by human neutrophils.", - "textContent": "257", + "textContent": "253", "type": [ "PublicationXref", "PubMed:458381" @@ -39472,7 +39472,7 @@ "id": "publicationXreffbb", "source": "J Biol Chem", "standardName": "Substrate specificities of 3-oxoacyl-CoA thiolase A and sterol carrier protein 2/3-oxoacyl-CoA thiolase purified from normal rat liver peroxisomes. Sterol carrier protein 2/3-oxoacyl-CoA thiolase is involved in the metabolism of 2-methyl-branched fatty acids and bile acid intermediates.", - "textContent": "190", + "textContent": "193", "type": [ "PublicationXref", "PubMed:9325339" @@ -39489,7 +39489,7 @@ "id": "publicationXreffc5", "source": "Cell Mol Life Sci", "standardName": "Molecular basis of homocysteine toxicity in humans.", - "textContent": "220", + "textContent": "103", "type": [ "PublicationXref", "PubMed:14999406" @@ -39508,7 +39508,7 @@ "id": "publicationXreffc9", "source": "Proc Natl Acad Sci U S A", "standardName": "Repression of the interleukin 6 gene promoter by p53 and the retinoblastoma susceptibility gene product.", - "textContent": "93", + "textContent": "26", "type": [ "PublicationXref", "PubMed:1652755" @@ -39528,7 +39528,7 @@ "id": "publicationXreffcb", "source": "Prostaglandins Leukot Essent Fatty Acids", "standardName": "In vivo conversion of linoleic acid to arachidonic acid in human adults.", - "textContent": "26", + "textContent": "181", "type": [ "PublicationXref", "PubMed:10471130" @@ -39547,7 +39547,7 @@ "id": "publicationXreffd4", "source": "J Physiol Pharmacol.", "standardName": "Nitric oxide and superoxide in inflammation and immune regulation.", - "textContent": "123", + "textContent": "275", "type": [ "PublicationXref", "PubMed:14726604" @@ -39565,7 +39565,7 @@ "id": "publicationXreffd5", "source": "Biochim Biophys Acta", "standardName": "Enzymatic sulphation of bile salts in human liver.", - "textContent": "255", + "textContent": "5", "type": [ "PublicationXref", "PubMed:698243" @@ -39583,7 +39583,7 @@ "id": "publicationXreffd7", "source": "Assay Drug Dev Technol", "standardName": "Farnesyl pyrophosphate synthase: real-time kinetics and inhibition by nitrogen-containing bisphosphonates in a scintillation assay.", - "textContent": "163", + "textContent": "284", "type": [ "PublicationXref", "PubMed:17477829" @@ -39606,7 +39606,7 @@ "id": "publicationXreffe6", "source": "Br J Nutr", "standardName": "Dietary intake of total marine n-3 polyunsaturated fatty acids, eicosapentaenoic acid, docosahexaenoic acid and docosapentaenoic acid and the risk of acute coronary syndrome - a cohort study.", - "textContent": "325", + "textContent": "158", "type": [ "PublicationXref", "PubMed:19825219" @@ -39623,7 +39623,7 @@ "id": "publicationXreffe7", "source": "Eur J Pediatr", "standardName": "The metabolism of homocysteine: pathways and regulation.", - "textContent": "194", + "textContent": "180", "type": [ "PublicationXref", "PubMed:9587024" @@ -39641,7 +39641,7 @@ "id": "publicationXreffec", "source": "Ann N Y Acad Sci", "standardName": "Free radicals and hearing. Cause, consequence, and criteria.", - "textContent": "28", + "textContent": "200", "type": [ "PublicationXref", "PubMed:10842581" @@ -39658,7 +39658,7 @@ "id": "publicationXrefff2", "source": "Ingenuity sofware", "standardName": "Arachidonic Acid Metabolism", - "textContent": "162", + "textContent": "185", "type": [ "PublicationXref" ], @@ -39676,7 +39676,7 @@ "id": "publicationXrefff7", "source": "J Biochem", "standardName": "Physiological role of D-3-hydroxyacyl-CoA dehydratase/D-3-hydroxyacyl-CoA dehydrogenase bifunctional protein.", - "textContent": "275", + "textContent": "45", "type": [ "PublicationXref", "PubMed:9133619" @@ -39697,7 +39697,7 @@ "id": "publicationXrefffd", "source": "Int J Biol Sci", "standardName": "Overexpression of selenoprotein H reduces Ht22 neuronal cell death after UVB irradiation by preventing superoxide formation.", - "textContent": "144", + "textContent": "313", "type": [ "PublicationXref", "PubMed:17389926" diff --git a/pathways/WP2848/WP2848.gpml b/pathways/WP2848/WP2848.gpml index e2487f4a7..a252219ba 100644 --- a/pathways/WP2848/WP2848.gpml +++ b/pathways/WP2848/WP2848.gpml @@ -3485,136 +3485,6 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - 21092735 - PubMed - 2-Methoxyestradiol inhibits the up-regulation of AQP4 and AQP1 expression after spinal cord injury. - Brain Res - 2011 - Wang YF - Fan ZK - Cao Y - Yu DS - Zhang YQ - Wang YS - - - 20202079 - PubMed - - - - 20202079 - PubMed - Eph receptor tyrosine kinases regulate astrocyte cytoskeletal rearrangement and focal adhesion formation. - J Neurochem - 2010 - Puschmann TB - Turnley AM - - - 22399755 - PubMed - Critical role of connexin 43 in secondary expansion of traumatic spinal cord injury. - J Neurosci - 2012 - Huang C - Han X - Li X - Lam E - Peng W - Lou N - Torres A - Yang M - Garre JM - Tian GF - Bennett MV - Nedergaard M - Takano T - - - 19932745 - PubMed - Astrocytes initiate inflammation in the injured mouse spinal cord by promoting the entry of neutrophils and inflammatory monocytes in an IL-1 receptor/MyD88-dependent fashion. - Brain Behav Immun - 2010 - Pineau I - Sun L - Bastien D - Lacroix S - - - 18267965 - PubMed - - - - 18267965 - PubMed - Greatly improved neurological outcome after spinal cord compression injury in AQP4-deficient mice. - Brain - 2008 - Saadoun S - Bell BA - Verkman AS - Papadopoulos MC - - - stem cell - CL:0000034 - Cell Type - - - 22930444 - PubMed - FOXO3a/p27kip1 expression and essential role after acute spinal cord injury in adult rat. - J Cell Biochem - 2013 - Zhang S - Huan W - Wei H - Shi J - Fan J - Zhao J - Shen A - Teng H - - - 16602711 - PubMed - Decoy peptides that bind dynorphin noncovalently prevent NMDA receptor-mediated neurotoxicity. - J Proteome Res - 2006 - Woods AS - Kaminski R - Oz M - Wang Y - Hauser K - Goody R - Wang HY - Jackson SN - Zeitz P - Zeitz KP - Zolkowska D - Schepers R - Nold M - Danielson J - Grأ¤slund A - Vukojevic V - Bakalkin G - Basbaum A - Shippenberg T - - - 17706365 - PubMed - The p75 neurotrophin receptor is essential for neuronal cell survival and improvement of functional recovery after spinal cord injury. - Neuroscience - 2007 - Chu GK - Yu W - Fehlings MG - 12666113 PubMed @@ -3638,41 +3508,32 @@ Proteins on this pathway have targeted assays available via the [https://assays. Hoffman EP Faden AI - - 20067580 + + 16498630 PubMed - 20067580 - PubMed - Involvement of ERK2 in traumatic spinal cord injury. - J Neurochem - 2010 - Yu CG - Yezierski RP - Joshi A - Raza K - Li Y - Geddes JW - - 19350383 - PubMed - - - - 19350383 + + 19770517 PubMed - Effects of long-term FK506 administration on functional and histopathological outcome after spinal cord injury in adult rat. - Cell Mol Neurobiol + Pathogenic antibodies are active participants in spinal cord injury. + J Clin Invest 2009 - Saganovأ، K - Orendأ،covأ، J - Sulla I Jr - Filipcأ­k P - Cأ­zkovأ، D - Vanickأ½ I + Dekaban GA + Thawer S + + + 21283639 + PubMed + Sustained delivery of activated Rho GTPases and BDNF promotes axon growth in CSPG-rich regions following spinal cord injury. + PLoS One + 2011 + Jain A + McKeon RJ + Brady-Kalnay SM + Bellamkonda RV 21868473 @@ -3700,89 +3561,186 @@ Proteins on this pathway have targeted assays available via the [https://assays. Kokotos G David S - - 10094148 - PubMed - Improved recovery after spinal cord trauma in ICAM-1 and P-selectin knockout mice. - Neuroreport - 1999 - Farooque M - Isaksson J - Olsson Y - - - 21657851 - PubMed - Prevention of both neutrophil and monocyte recruitment promotes recovery after spinal cord injury. - J Neurotrauma - 2011 - 21657851 + + 20202079 PubMed - Prevention of both neutrophil and monocyte recruitment promotes recovery after spinal cord injury. - J Neurotrauma - 2011 - 21657851 + + + + 20202079 PubMed - Prevention of both neutrophil and monocyte recruitment promotes recovery after spinal cord injury. - J Neurotrauma - 2011 - Lee SM - Rosen S - Weinstein P - van Rooijen N - Noble-Haeusslein LJ + Eph receptor tyrosine kinases regulate astrocyte cytoskeletal rearrangement and focal adhesion formation. + J Neurochem + 2010 + Puschmann TB + Turnley AM - - regulatory pathway - PW:0000004 - Pathway Ontology - - - 22884909 + + 11553680 PubMed - Characterization of inflammatory gene expression and galectin-3 function after spinal cord injury in mice. - Brain Res - 2012 - Pajoohesh-Ganji A - Knoblach SM - Faden AI - Byrnes KR + A neutrophil elastase inhibitor (ONO-5046) reduces neurologic damage after spinal cord injury in rats. + J Neurochem + 2001 + Tonai T + Shiba K + Taketani Y + Ohmoto Y + Murata K + Muraguchi M + Ohsaki H + Takeda E + Nishisho T - - oligodendrocyte - CL:0000128 - Cell Type - - - 21168495 + + 17917587 PubMed - CD47 knockout mice exhibit improved recovery from spinal cord injury. - Neurobiol Dis + Annexin A1 reduces inflammatory reaction and tissue damage through inhibition of phospholipase A2 activation in adult rats following spinal cord injury. + J Neuropathol Exp Neurol + 2007 + Liu NK + Zhang YP + Han S + Pei J + Xu LY + Lu PH + Shields CB + Xu XM + + + 19342987 + PubMed + Sudden Infant Death Syndrome and Sudden Intrauterine Unexplained Death: Correlation Between Hypoplasia of Raphأƒآ¢أ‚آˆأ‚آڑأƒآکأ‚آ¬أƒآ¯أ‚آ؟أ‚آ½أƒآژأ‚آ©أƒآ¢أ‚آˆأ‚آڑأƒآکأ‚آ¬أƒآ¯أ‚آ؟أ‚آ½أƒآژأ‚آ©أƒآژأ‚آ© Nuclei and Serotonin Transporter Gene Promoter Polymorphism. + Pediatr Res + 2009 + Lavezzi AM + Casale V + Oneda R + Weese-Mayer DE + Matturri L + + + 20067580 + PubMed + + + + 20067580 + PubMed + Involvement of ERK2 in traumatic spinal cord injury. + J Neurochem + 2010 + Yu CG + Yezierski RP + Joshi A + Raza K + Li Y + Geddes JW + + + spinal cord disease + DOID:319 + Disease + + + 21640756 + PubMed + Current and future therapeutic strategies for functional repair of spinal cord injury. + Pharmacol Ther 2011 - Myers SA - DeVries WH - Andres KR - Gruenthal MJ - Benton RL - Hoying JB - Hagg T - Whittemore SR + Tohda C + Kuboyama T - - 17621255 + + 20304963 PubMed - TNF-alpha blockage in a mouse model of SCI: evidence for improved outcome. - Shock - 2008 - Genovese T - Mazzon E - Crisafulli C - Di Paola R - Muiأ  C - Esposito E - Bramanti P - Cuzzocrea S + The LTB4-BLT1 axis mediates neutrophil infiltration and secondary injury in experimental spinal cord injury. + Am J Pathol + 2010 + Saiwai H + Ohkawa Y + Yamada H + Kumamaru H + Harada A + Okano H + Yokomizo T + Iwamoto Y + Okada S + + + 18637713 + PubMed + Alterations in the expression of the apurinic/apyrimidinic endonuclease-1/redox factor-1 (APE/ref-1) and DNA damage in the caudal region of acute and chronic spinal cord injured rats treated by embryonic neural stem cells. + Physiol Res + 2009 + DAGCI T + ARMAGAN G + KONYALIOGLU S + YALCIN A + + + 11059815 + PubMed + Glial fibrillary acidic protein: GFAP-thirty-one years (1969-2000). + Neurochem Res + 2000 + Eng LF + Ghirnikar RS + Lee YL + + growth factor signaling pathway + PW:0000168 + Pathway Ontology + + + 21092735 + PubMed + 2-Methoxyestradiol inhibits the up-regulation of AQP4 and AQP1 expression after spinal cord injury. + Brain Res + 2011 + Wang YF + Fan ZK + Cao Y + Yu DS + Zhang YQ + Wang YS + + + 16602711 + PubMed + Decoy peptides that bind dynorphin noncovalently prevent NMDA receptor-mediated neurotoxicity. + J Proteome Res + 2006 + Woods AS + Kaminski R + Oz M + Wang Y + Hauser K + Goody R + Wang HY + Jackson SN + Zeitz P + Zeitz KP + Zolkowska D + Schepers R + Nold M + Danielson J + Grأ¤slund A + Vukojevic V + Bakalkin G + Basbaum A + Shippenberg T + + + regulatory pathway + PW:0000004 + Pathway Ontology + + + traumatic neurosis + DOID:2055 + Disease + 17567803 PubMed @@ -3793,34 +3751,71 @@ Proteins on this pathway have targeted assays available via the [https://assays. Pernold K Olson L - - 21957482 + + 21673720 PubMed - Activated microglia inhibit axonal growth through RGMa. - PLoS One + Repertoire of microglial and macrophage responses after spinal cord injury. + Nat Rev Neurosci 2011 - 21957482 + David S + Kroner A + + + 19932745 PubMed - Activated microglia inhibit axonal growth through RGMa. - PLoS One - 2011 - Kitayama M - Ueno M - Itakura T - Yamashita T + Astrocytes initiate inflammation in the injured mouse spinal cord by promoting the entry of neutrophils and inflammatory monocytes in an IL-1 receptor/MyD88-dependent fashion. + Brain Behav Immun + 2010 + Pineau I + Sun L + Bastien D + Lacroix S - - 19770517 + + 11585624 PubMed - Pathogenic antibodies are active participants in spinal cord injury. - J Clin Invest + AIF-1 expression defines a proliferating and alert microglial/macrophage phenotype following spinal cord injury in rats. + J Neuroimmunol + 2001 + Schwab JM + Frei E + Klusman I + Schnell L + Schwab ME + Schluesener HJ + + + 19350383 + PubMed + + + + 19350383 + PubMed + Effects of long-term FK506 administration on functional and histopathological outcome after spinal cord injury in adult rat. + Cell Mol Neurobiol 2009 - Dekaban GA - Thawer S + Saganovأ، K + Orendأ،covأ، J + Sulla I Jr + Filipcأ­k P + Cأ­zkovأ، D + Vanickأ½ I + + + 22884909 + PubMed + Characterization of inflammatory gene expression and galectin-3 function after spinal cord injury in mice. + Brain Res + 2012 + Pajoohesh-Ganji A + Knoblach SM + Faden AI + Byrnes KR - astrocyte of the spinal cord - CL:0002606 + oligodendrocyte + CL:0000128 Cell Type @@ -3844,19 +3839,11 @@ Proteins on this pathway have targeted assays available via the [https://assays. Huebner E Strittmatter SM - - 22564823 - PubMed - PlexinA2 limits recovery from corticospinal axotomy by mediating oligodendrocyte-derived Sema6A growth inhibition. - Mol Cell Neurosci - 2012 - Shim SO - Cafferty WB - Schmidt EC - Kim BG - Fujisawa H - Strittmatter SM - + + keratinocyte + CL:0000312 + Cell Type + 17482149 PubMed @@ -3876,112 +3863,104 @@ Proteins on this pathway have targeted assays available via the [https://assays. Xie MJ Wang W - - 20304963 - PubMed - The LTB4-BLT1 axis mediates neutrophil infiltration and secondary injury in experimental spinal cord injury. - Am J Pathol - 2010 - Saiwai H - Ohkawa Y - Yamada H - Kumamaru H - Harada A - Okano H - Yokomizo T - Iwamoto Y - Okada S - - - 16504406 - PubMed - Macrophage migration inhibitory factor induces cell death and decreases neuronal nitric oxide expression in spinal cord neurons. - Neuroscience - 2006 - Chalimoniuk M - King-Pospisil K - Metz CN - Toborek M - - - 16498630 + + 12861073 PubMed + 12861073 + PubMed + Axonal plasticity and functional recovery after spinal cord injury in mice deficient in both glial fibrillary acidic protein and vimentin genes. + Proc Natl Acad Sci U S A + 2003 + Menet V + Prieto M + Privat A + Gimأ©nez y Ribotta M - - 9872457 + + 22399755 PubMed - Role of cyclooxygenase 2 in acute spinal cord injury. + Critical role of connexin 43 in secondary expansion of traumatic spinal cord injury. + J Neurosci + 2012 + Huang C + Han X + Li X + Lam E + Peng W + Lou N + Torres A + Yang M + Garre JM + Tian GF + Bennett MV + Nedergaard M + Takano T + + + 21657851 + PubMed + Prevention of both neutrophil and monocyte recruitment promotes recovery after spinal cord injury. + J Neurotrauma + 2011 + 21657851 + PubMed + Prevention of both neutrophil and monocyte recruitment promotes recovery after spinal cord injury. + J Neurotrauma + 2011 + 21657851 + PubMed + Prevention of both neutrophil and monocyte recruitment promotes recovery after spinal cord injury. J Neurotrauma - 1998 - Resnick DK - Graham SH - Dixon CE - Marion DW + 2011 + Lee SM + Rosen S + Weinstein P + van Rooijen N + Noble-Haeusslein LJ - - 21161717 + + 19061375 PubMed - spinal cord motor neuron - CL:0011001 + myoblast + CL:0000056 Cell Type - - 11059815 - PubMed - Glial fibrillary acidic protein: GFAP-thirty-one years (1969-2000). - Neurochem Res - 2000 - Eng LF - Ghirnikar RS - Lee YL - - - 18637713 + + 17629414 PubMed - Alterations in the expression of the apurinic/apyrimidinic endonuclease-1/redox factor-1 (APE/ref-1) and DNA damage in the caudal region of acute and chronic spinal cord injured rats treated by embryonic neural stem cells. - Physiol Res - 2009 - DAGCI T - ARMAGAN G - KONYALIOGLU S - YALCIN A + Neuropsin promotes oligodendrocyte death, demyelination and axonal degeneration after spinal cord injury. + Neuroscience + 2007 + Terayama R + Bando Y + Murakami K + Kato K + Kishibe M + Yoshida S - - 11585624 + + 23027386 PubMed - AIF-1 expression defines a proliferating and alert microglial/macrophage phenotype following spinal cord injury in rats. - J Neuroimmunol - 2001 - Schwab JM - Frei E - Klusman I - Schnell L - Schwab ME - Schluesener HJ - - - 11553680 + + + + 23027386 PubMed - A neutrophil elastase inhibitor (ONO-5046) reduces neurologic damage after spinal cord injury in rats. - J Neurochem - 2001 - Tonai T - Shiba K - Taketani Y - Ohmoto Y - Murata K - Muraguchi M - Ohsaki H - Takeda E - Nishisho T + Conditional Sox9 ablation reduces chondroitin sulfate proteoglycan levels and improves motor function following spinal cord injury. + Glia + 2013 + McKillop WM + Dragan M + Schedl A + Brown A 20547125 @@ -4003,6 +3982,27 @@ Proteins on this pathway have targeted assays available via the [https://assays. Kang B Zheng B + + neural stem cell + CL:0000047 + Cell Type + + + 18267965 + PubMed + + + + 18267965 + PubMed + Greatly improved neurological outcome after spinal cord compression injury in AQP4-deficient mice. + Brain + 2008 + Saadoun S + Bell BA + Verkman AS + Papadopoulos MC + 22536415 PubMed @@ -4013,160 +4013,75 @@ Proteins on this pathway have targeted assays available via the [https://assays. Gonzأ،lez P Rodriguez FJ - - 21673720 - PubMed - Repertoire of microglial and macrophage responses after spinal cord injury. - Nat Rev Neurosci - 2011 - David S - Kroner A - - - 17629414 - PubMed - Neuropsin promotes oligodendrocyte death, demyelination and axonal degeneration after spinal cord injury. - Neuroscience - 2007 - Terayama R - Bando Y - Murakami K - Kato K - Kishibe M - Yoshida S - - - 23035104 + + 21161717 PubMed - 23035104 - PubMed - p53 Regulates the neuronal intrinsic and extrinsic responses affecting the recovery of motor function following spinal cord injury. - J Neurosci - 2012 - Floriddia EM - Rathore KI - Tedeschi A - Quadrato G - Wuttke A - Lueckmann JM - Kigerl KA - Popovich PG - Di Giovanni S - - - neural stem cell - CL:0000047 - Cell Type - - - 21373950 + 21161717 PubMed - Cell cycle activation and spinal cord injury. - Neurotherapeutics + Early microvascular reactions and blood-spinal cord barrier disruption are instrumental in pathophysiology of spinal cord injury and repair: novel therapeutic strategies including nanowired drug delivery to enhance neuroprotection. + J Neural Transm 2011 - Wu J - Stoica BA - Faden AI - - - traumatic neurosis - DOID:2055 - Disease - - - 19342987 - PubMed - Sudden Infant Death Syndrome and Sudden Intrauterine Unexplained Death: Correlation Between Hypoplasia of Raphأƒآ¢أ‚آˆأ‚آڑأƒآکأ‚آ¬أƒآ¯أ‚آ؟أ‚آ½أƒآژأ‚آ©أƒآ¢أ‚آˆأ‚آڑأƒآکأ‚آ¬أƒآ¯أ‚آ؟أ‚آ½أƒآژأ‚آ©أƒآژأ‚آ© Nuclei and Serotonin Transporter Gene Promoter Polymorphism. - Pediatr Res - 2009 - Lavezzi AM - Casale V - Oneda R - Weese-Mayer DE - Matturri L - - - 22884909 - PubMed - Characterization of inflammatory gene expression and galectin-3 function after spinal cord injury in mice. - Brain Res - 2012 - Pajoohesh-Ganji A - Knoblach SM - Faden AI - Byrnes KR + Sharma HS - - 21640756 + + 16504406 PubMed - Current and future therapeutic strategies for functional repair of spinal cord injury. - Pharmacol Ther - 2011 - Tohda C - Kuboyama T + Macrophage migration inhibitory factor induces cell death and decreases neuronal nitric oxide expression in spinal cord neurons. + Neuroscience + 2006 + Chalimoniuk M + King-Pospisil K + Metz CN + Toborek M - - 12861073 + + 23152062 PubMed - 12861073 - PubMed - Axonal plasticity and functional recovery after spinal cord injury in mice deficient in both glial fibrillary acidic protein and vimentin genes. - Proc Natl Acad Sci U S A - 2003 - Menet V - Prieto M - Privat A - Gimأ©nez y Ribotta M - - - myoblast - CL:0000056 - Cell Type - - - 17917587 + 23152062 PubMed - Annexin A1 reduces inflammatory reaction and tissue damage through inhibition of phospholipase A2 activation in adult rats following spinal cord injury. - J Neuropathol Exp Neurol - 2007 - Liu NK - Zhang YP - Han S - Pei J - Xu LY - Lu PH - Shields CB - Xu XM + Molecular targeting of NOX4 for neuropathic pain after traumatic injury of the spinal cord. + Cell Death Dis + 2012 + Im YB + Jee MK + Choi JI + Cho HT + Kwon OH + Kang SK - - 16295699 + + 21161717 PubMed - Stimulation of production of glial cell line-derived neurotrophic factor and nitric oxide by lipopolysaccharide with different dose-responsiveness in cultured rat macrophages. - Biomed Res - 2005 - Hashimoto M - Ito T - Fukumitsu H - Nomoto H - Furukawa Y - Furukawa S + + + - spinal cord disease - DOID:319 - Disease - - - keratinocyte - CL:0000312 + stem cell + CL:0000034 Cell Type + + 21168495 + PubMed + CD47 knockout mice exhibit improved recovery from spinal cord injury. + Neurobiol Dis + 2011 + Myers SA + DeVries WH + Andres KR + Gruenthal MJ + Benton RL + Hoying JB + Hagg T + Whittemore SR + 16623828 PubMed @@ -4185,29 +4100,52 @@ Proteins on this pathway have targeted assays available via the [https://assays. Brennan C Bolsover S - - 23027386 + + 17621255 PubMed - - - - 23027386 + TNF-alpha blockage in a mouse model of SCI: evidence for improved outcome. + Shock + 2008 + Genovese T + Mazzon E + Crisafulli C + Di Paola R + Muiأ  C + Esposito E + Bramanti P + Cuzzocrea S + + + 22930444 PubMed - Conditional Sox9 ablation reduces chondroitin sulfate proteoglycan levels and improves motor function following spinal cord injury. - Glia + FOXO3a/p27kip1 expression and essential role after acute spinal cord injury in adult rat. + J Cell Biochem 2013 - McKillop WM - Dragan M - Schedl A - Brown A + Zhang S + Huan W + Wei H + Shi J + Fan J + Zhao J + Shen A + Teng H - - 19061375 + + 22884909 PubMed - - - + Characterization of inflammatory gene expression and galectin-3 function after spinal cord injury in mice. + Brain Res + 2012 + Pajoohesh-Ganji A + Knoblach SM + Faden AI + Byrnes KR + + astrocyte of the spinal cord + CL:0002606 + Cell Type + 22771695 PubMed @@ -4226,18 +4164,6 @@ Proteins on this pathway have targeted assays available via the [https://assays. Raؤچekovأ، E Vanickأ½ I - - 19770513 - PubMed - - - - - - growth factor signaling pathway - PW:0000168 - Pathway Ontology - 17698296 PubMed @@ -4252,18 +4178,94 @@ Proteins on this pathway have targeted assays available via the [https://assays. Scheff SW Knapp PE - - 21161717 + + 21771809 + PubMed + Interplay between Wnt2 and Wnt2bb controls multiple steps of early foregut-derived organ development. + Development + 2011 + Poulain M + Ober EA + + + 23035104 PubMed - 21161717 + 23035104 PubMed - Early microvascular reactions and blood-spinal cord barrier disruption are instrumental in pathophysiology of spinal cord injury and repair: novel therapeutic strategies including nanowired drug delivery to enhance neuroprotection. - J Neural Transm + p53 Regulates the neuronal intrinsic and extrinsic responses affecting the recovery of motor function following spinal cord injury. + J Neurosci + 2012 + Floriddia EM + Rathore KI + Tedeschi A + Quadrato G + Wuttke A + Lueckmann JM + Kigerl KA + Popovich PG + Di Giovanni S + + + 9872457 + PubMed + Role of cyclooxygenase 2 in acute spinal cord injury. + J Neurotrauma + 1998 + Resnick DK + Graham SH + Dixon CE + Marion DW + + + 21373950 + PubMed + Cell cycle activation and spinal cord injury. + Neurotherapeutics 2011 - Sharma HS + Wu J + Stoica BA + Faden AI + + + 19770513 + PubMed + + + + + + 21957482 + PubMed + Activated microglia inhibit axonal growth through RGMa. + PLoS One + 2011 + 21957482 + PubMed + Activated microglia inhibit axonal growth through RGMa. + PLoS One + 2011 + Kitayama M + Ueno M + Itakura T + Yamashita T + + + spinal cord motor neuron + CL:0011001 + Cell Type + + + 17706365 + PubMed + The p75 neurotrophin receptor is essential for neuronal cell survival and improvement of functional recovery after spinal cord injury. + Neuroscience + 2007 + Chu GK + Yu W + Fehlings MG 23045704 @@ -4286,43 +4288,41 @@ Proteins on this pathway have targeted assays available via the [https://assays. French DL Weiss MJ - - 21283639 + + 22564823 PubMed - Sustained delivery of activated Rho GTPases and BDNF promotes axon growth in CSPG-rich regions following spinal cord injury. - PLoS One - 2011 - Jain A - McKeon RJ - Brady-Kalnay SM - Bellamkonda RV + PlexinA2 limits recovery from corticospinal axotomy by mediating oligodendrocyte-derived Sema6A growth inhibition. + Mol Cell Neurosci + 2012 + Shim SO + Cafferty WB + Schmidt EC + Kim BG + Fujisawa H + Strittmatter SM - - 23152062 - PubMed - - - - 23152062 + + 16295699 PubMed - Molecular targeting of NOX4 for neuropathic pain after traumatic injury of the spinal cord. - Cell Death Dis - 2012 - Im YB - Jee MK - Choi JI - Cho HT - Kwon OH - Kang SK + Stimulation of production of glial cell line-derived neurotrophic factor and nitric oxide by lipopolysaccharide with different dose-responsiveness in cultured rat macrophages. + Biomed Res + 2005 + Hashimoto M + Ito T + Fukumitsu H + Nomoto H + Furukawa Y + Furukawa S - - 21771809 + + 10094148 PubMed - Interplay between Wnt2 and Wnt2bb controls multiple steps of early foregut-derived organ development. - Development - 2011 - Poulain M - Ober EA + Improved recovery after spinal cord trauma in ICAM-1 and P-selectin knockout mice. + Neuroreport + 1999 + Farooque M + Isaksson J + Olsson Y diff --git a/pathways/WP2848/WP2848.json b/pathways/WP2848/WP2848.json index 47927465f..51b8d782c 100644 --- a/pathways/WP2848/WP2848.json +++ b/pathways/WP2848/WP2848.json @@ -37465,7 +37465,7 @@ "id": "publicationXrefa11", "source": "J Cell Biochem", "standardName": "FOXO3a/p27kip1 expression and essential role after acute spinal cord injury in adult rat.", - "textContent": "45", + "textContent": "54", "type": [ "PublicationXref", "PubMed:22930444" @@ -37485,7 +37485,7 @@ "id": "publicationXrefa26", "source": "J Neurosci", "standardName": "MAG and OMgp synergize with Nogo-A to restrict axonal growth and neurological recovery after spinal cord trauma.", - "textContent": "27", + "textContent": "29", "type": [ "PublicationXref", "PubMed:20484625" @@ -37497,7 +37497,7 @@ "publicationXrefaa6": { "gpmlElementName": "PublicationXref", "id": "publicationXrefaa6", - "textContent": "47", + "textContent": "51", "type": [ "PublicationXref", "PubMed:21161717" @@ -37520,7 +37520,7 @@ "id": "publicationXrefab0", "source": "Neurobiol Dis", "standardName": "CD47 knockout mice exhibit improved recovery from spinal cord injury.", - "textContent": "33", + "textContent": "38", "type": [ "PublicationXref", "PubMed:21168495" @@ -37550,7 +37550,7 @@ "id": "publicationXrefaba", "source": "Proc Natl Acad Sci U S A", "standardName": "Trisomy 21-associated defects in human primitive hematopoiesis revealed through induced pluripotent stem cells.", - "textContent": "54", + "textContent": "48", "type": [ "PublicationXref", "PubMed:23045704" @@ -37570,7 +37570,7 @@ "id": "publicationXrefabd", "source": "J Neurotrauma", "standardName": "Role of cyclooxygenase 2 in acute spinal cord injury.", - "textContent": "1", + "textContent": "3", "type": [ "PublicationXref", "PubMed:9872457" @@ -37589,7 +37589,7 @@ "id": "publicationXrefabe", "source": "J Neurosci", "standardName": "Inhibiting epidermal growth factor receptor improves structural, locomotor, sensory, and bladder recovery from experimental spinal cord injury.", - "textContent": "13", + "textContent": "14", "type": [ "PublicationXref", "PubMed:17567803" @@ -37609,7 +37609,7 @@ "id": "publicationXrefad1", "source": "PLoS One", "standardName": "Activated microglia inhibit axonal growth through RGMa.", - "textContent": "34", + "textContent": "40", "type": [ "PublicationXref", "PubMed:21957482" @@ -37633,7 +37633,7 @@ "id": "publicationXrefad5", "source": "Shock", "standardName": "TNF-alpha blockage in a mouse model of SCI: evidence for improved outcome.", - "textContent": "19", + "textContent": "20", "type": [ "PublicationXref", "PubMed:17621255" @@ -37668,7 +37668,7 @@ "id": "publicationXrefaef", "source": "J Proteome Res", "standardName": "Decoy peptides that bind dynorphin noncovalently prevent NMDA receptor-mediated neurotoxicity.", - "textContent": "9", + "textContent": "10", "type": [ "PublicationXref", "PubMed:16602711" @@ -37687,7 +37687,7 @@ "id": "publicationXrefb55", "source": "Neurochem Res", "standardName": "Glial fibrillary acidic protein: GFAP-thirty-one years (1969-2000).", - "textContent": "3", + "textContent": "5", "type": [ "PublicationXref", "PubMed:11059815" @@ -37709,7 +37709,7 @@ "id": "publicationXrefb6f", "source": "Cell Mol Neurobiol", "standardName": "Effects of long-term FK506 administration on functional and histopathological outcome after spinal cord injury in adult rat.", - "textContent": "20", + "textContent": "24", "type": [ "PublicationXref", "PubMed:19350383" @@ -37731,7 +37731,7 @@ "id": "publicationXrefb75", "source": "Ann Neurol", "standardName": "Gene profiling in spinal cord injury shows role of cell cycle in neuronal death.", - "textContent": "6", + "textContent": "1", "type": [ "PublicationXref", "PubMed:12666113" @@ -37755,7 +37755,7 @@ "id": "publicationXrefb9b", "source": "Neuron", "standardName": "Assessing spinal axon regeneration and sprouting in Nogo-, MAG-, and OMgp-deficient mice.", - "textContent": "29", + "textContent": "30", "type": [ "PublicationXref", "PubMed:20547125" @@ -37777,7 +37777,7 @@ "id": "publicationXrefbc0", "source": "Life Sci", "standardName": "Immunosuppressant FK506: focusing on neuroprotective effects following brain and spinal cord injury.", - "textContent": "52", + "textContent": "53", "type": [ "PublicationXref", "PubMed:22771695" @@ -37796,7 +37796,7 @@ "id": "publicationXrefbc2", "source": "Neuroscience", "standardName": "The p75 neurotrophin receptor is essential for neuronal cell survival and improvement of functional recovery after spinal cord injury.", - "textContent": "12", + "textContent": "18", "type": [ "PublicationXref", "PubMed:17706365" @@ -37819,7 +37819,7 @@ "id": "publicationXrefbd3", "source": "Brain Res", "standardName": "Attenuation of astrogliosis by suppressing of microglial proliferation with the cell cycle inhibitor olomoucine in rat spinal cord injury model.", - "textContent": "14", + "textContent": "15", "type": [ "PublicationXref", "PubMed:17482149" @@ -37844,7 +37844,7 @@ "id": "publicationXrefbd9", "source": "J Neurochem", "standardName": "A neutrophil elastase inhibitor (ONO-5046) reduces neurologic damage after spinal cord injury in rats.", - "textContent": "5", + "textContent": "6", "type": [ "PublicationXref", "PubMed:11553680" @@ -37873,7 +37873,7 @@ "id": "publicationXrefc0d", "source": "J Neurosci", "standardName": "Critical role of connexin 43 in secondary expansion of traumatic spinal cord injury.", - "textContent": "41", + "textContent": "42", "type": [ "PublicationXref", "PubMed:22399755" @@ -37892,7 +37892,7 @@ "id": "publicationXrefc5f", "source": "PLoS One", "standardName": "Acute leptin treatment enhances functional recovery after spinal cord injury.", - "textContent": "48", + "textContent": "45", "type": [ "PublicationXref", "PubMed:22536415" @@ -37914,7 +37914,7 @@ "id": "publicationXrefc8a", "source": "Neuroscience", "standardName": "Neuropsin promotes oligodendrocyte death, demyelination and axonal degeneration after spinal cord injury.", - "textContent": "15", + "textContent": "16", "type": [ "PublicationXref", "PubMed:17629414" @@ -37926,7 +37926,7 @@ "publicationXrefcae": { "gpmlElementName": "PublicationXref", "id": "publicationXrefcae", - "textContent": "46", + "textContent": "2", "type": [ "PublicationXref", "PubMed:16498630" @@ -37946,7 +37946,7 @@ "id": "publicationXrefcd2", "source": "Pediatr Res", "standardName": "Sudden Infant Death Syndrome and Sudden Intrauterine Unexplained Death: Correlation Between Hypoplasia of Raphأƒآ¢أ‚آˆأ‚آڑأƒآکأ‚آ¬أƒآ¯أ‚آ؟أ‚آ½أƒآژأ‚آ©أƒآ¢أ‚آˆأ‚آڑأƒآکأ‚آ¬أƒآ¯أ‚آ؟أ‚آ½أƒآژأ‚آ©أƒآژأ‚آ© Nuclei and Serotonin Transporter Gene Promoter Polymorphism.", - "textContent": "23", + "textContent": "22", "type": [ "PublicationXref", "PubMed:19342987" @@ -37986,7 +37986,7 @@ "id": "publicationXrefd33", "source": "Neuroscience", "standardName": "Macrophage migration inhibitory factor induces cell death and decreases neuronal nitric oxide expression in spinal cord neurons.", - "textContent": "10", + "textContent": "11", "type": [ "PublicationXref", "PubMed:16504406" @@ -38006,7 +38006,7 @@ "id": "publicationXrefd54", "source": "Physiol Res", "standardName": "Alterations in the expression of the apurinic/apyrimidinic endonuclease-1/redox factor-1 (APE/ref-1) and DNA damage in the caudal region of acute and chronic spinal cord injured rats treated by embryonic neural stem cells.", - "textContent": "22", + "textContent": "23", "type": [ "PublicationXref", "PubMed:18637713" @@ -38018,7 +38018,7 @@ "publicationXrefd57": { "gpmlElementName": "PublicationXref", "id": "publicationXrefd57", - "textContent": "51", + "textContent": "43", "type": [ "PublicationXref", "PubMed:19061375" @@ -38047,7 +38047,7 @@ "id": "publicationXrefd81", "source": "FASEB J", "standardName": "Phospholipase A2 superfamily members play divergent roles after spinal cord injury.", - "textContent": "31", + "textContent": "32", "type": [ "PublicationXref", "PubMed:21868473" @@ -38068,7 +38068,7 @@ "id": "publicationXrefd87", "source": "J Neurotrauma", "standardName": "Prevention of both neutrophil and monocyte recruitment promotes recovery after spinal cord injury.", - "textContent": "32", + "textContent": "36", "type": [ "PublicationXref", "PubMed:21657851" @@ -38090,7 +38090,7 @@ "id": "publicationXrefda7", "source": "Mol Cell Neurosci", "standardName": "PlexinA2 limits recovery from corticospinal axotomy by mediating oligodendrocyte-derived Sema6A growth inhibition.", - "textContent": "43", + "textContent": "49", "type": [ "PublicationXref", "PubMed:22564823" @@ -38110,7 +38110,7 @@ "id": "publicationXrefdad", "source": "Brain", "standardName": "Greatly improved neurological outcome after spinal cord compression injury in AQP4-deficient mice.", - "textContent": "18", + "textContent": "19", "type": [ "PublicationXref", "PubMed:18267965" @@ -38132,7 +38132,7 @@ "id": "publicationXrefdb9", "source": "Brain Res", "standardName": "2-Methoxyestradiol inhibits the up-regulation of AQP4 and AQP1 expression after spinal cord injury.", - "textContent": "30", + "textContent": "34", "type": [ "PublicationXref", "PubMed:21092735" @@ -38170,7 +38170,7 @@ "id": "publicationXrefe0c", "source": "Brain Behav Immun", "standardName": "Astrocytes initiate inflammation in the injured mouse spinal cord by promoting the entry of neutrophils and inflammatory monocytes in an IL-1 receptor/MyD88-dependent fashion.", - "textContent": "25", + "textContent": "28", "type": [ "PublicationXref", "PubMed:19932745" @@ -38190,7 +38190,7 @@ "id": "publicationXrefe7b", "source": "Brain Res", "standardName": "Characterization of inflammatory gene expression and galectin-3 function after spinal cord injury in mice.", - "textContent": "42", + "textContent": "41", "type": [ "PublicationXref", "PubMed:22884909" @@ -38234,7 +38234,7 @@ "id": "publicationXrefe9c", "source": "J Neuroimmunol", "standardName": "AIF-1 expression defines a proliferating and alert microglial/macrophage phenotype following spinal cord injury in rats.", - "textContent": "4", + "textContent": "7", "type": [ "PublicationXref", "PubMed:11585624" @@ -38258,7 +38258,7 @@ "id": "publicationXrefea4", "source": "J Neuropathol Exp Neurol", "standardName": "Annexin A1 reduces inflammatory reaction and tissue damage through inhibition of phospholipase A2 activation in adult rats following spinal cord injury.", - "textContent": "16", + "textContent": "13", "type": [ "PublicationXref", "PubMed:17917587" @@ -38278,7 +38278,7 @@ "id": "publicationXrefeac", "source": "PLoS One", "standardName": "Sustained delivery of activated Rho GTPases and BDNF promotes axon growth in CSPG-rich regions following spinal cord injury.", - "textContent": "39", + "textContent": "31", "type": [ "PublicationXref", "PubMed:21283639" @@ -38295,7 +38295,7 @@ "id": "publicationXrefeb2", "source": "J Neural Transm", "standardName": "Early microvascular reactions and blood-spinal cord barrier disruption are instrumental in pathophysiology of spinal cord injury and repair: novel therapeutic strategies including nanowired drug delivery to enhance neuroprotection.", - "textContent": "38", + "textContent": "37", "type": [ "PublicationXref", "PubMed:21161717" @@ -38314,7 +38314,7 @@ "id": "publicationXrefebb", "source": "Neurotherapeutics", "standardName": "Cell cycle activation and spinal cord injury.", - "textContent": "36", + "textContent": "39", "type": [ "PublicationXref", "PubMed:21373950" @@ -38336,7 +38336,7 @@ "id": "publicationXrefec6", "source": "Eur J Neurosci", "standardName": "Accumulation of the inhibitory receptor EphA4 may prevent regeneration of corticospinal tract axons following lesion.", - "textContent": "11", + "textContent": "12", "type": [ "PublicationXref", "PubMed:16623828" @@ -38358,7 +38358,7 @@ "id": "publicationXrefef0", "source": "Cell Death Dis", "standardName": "Molecular targeting of NOX4 for neuropathic pain after traumatic injury of the spinal cord.", - "textContent": "55", + "textContent": "46", "type": [ "PublicationXref", "PubMed:23152062" @@ -38377,7 +38377,7 @@ "id": "publicationXreff1e", "source": "Neuroreport", "standardName": "Improved recovery after spinal cord trauma in ICAM-1 and P-selectin knockout mice.", - "textContent": "2", + "textContent": "4", "type": [ "PublicationXref", "PubMed:10094148" @@ -38395,7 +38395,7 @@ "id": "publicationXreff35", "source": "Pharmacol Ther", "standardName": "Current and future therapeutic strategies for functional repair of spinal cord injury.", - "textContent": "37", + "textContent": "33", "type": [ "PublicationXref", "PubMed:21640756" @@ -38420,7 +38420,7 @@ "id": "publicationXreff41", "source": "Am J Pathol", "standardName": "The LTB4-BLT1 axis mediates neutrophil infiltration and secondary injury in experimental spinal cord injury.", - "textContent": "28", + "textContent": "27", "type": [ "PublicationXref", "PubMed:20304963" @@ -38458,7 +38458,7 @@ "id": "publicationXreff6b", "source": "Proc Natl Acad Sci U S A", "standardName": "Axonal plasticity and functional recovery after spinal cord injury in mice deficient in both glial fibrillary acidic protein and vimentin genes.", - "textContent": "7", + "textContent": "8", "type": [ "PublicationXref", "PubMed:12861073" @@ -38476,7 +38476,7 @@ "id": "publicationXreff76", "source": "J Neurochem", "standardName": "Eph receptor tyrosine kinases regulate astrocyte cytoskeletal rearrangement and focal adhesion formation.", - "textContent": "24", + "textContent": "25", "type": [ "PublicationXref", "PubMed:20202079" @@ -38496,7 +38496,7 @@ "id": "publicationXreff7f", "source": "Brain Res", "standardName": "Characterization of inflammatory gene expression and galectin-3 function after spinal cord injury in mice.", - "textContent": "49", + "textContent": "52", "type": [ "PublicationXref", "PubMed:22884909" @@ -38514,7 +38514,7 @@ "id": "publicationXreff80", "source": "Development", "standardName": "Interplay between Wnt2 and Wnt2bb controls multiple steps of early foregut-derived organ development.", - "textContent": "40", + "textContent": "44", "type": [ "PublicationXref", "PubMed:21771809" @@ -38539,7 +38539,7 @@ "id": "publicationXreff8f", "source": "J Neurosci", "standardName": "p53 Regulates the neuronal intrinsic and extrinsic responses affecting the recovery of motor function following spinal cord injury.", - "textContent": "44", + "textContent": "47", "type": [ "PublicationXref", "PubMed:23035104" @@ -38551,7 +38551,7 @@ "publicationXreff97": { "gpmlElementName": "PublicationXref", "id": "publicationXreff97", - "textContent": "53", + "textContent": "55", "type": [ "PublicationXref", "PubMed:19770513" @@ -38572,7 +38572,7 @@ "id": "publicationXreffce", "source": "Biomed Res", "standardName": "Stimulation of production of glial cell line-derived neurotrophic factor and nitric oxide by lipopolysaccharide with different dose-responsiveness in cultured rat macrophages.", - "textContent": "8", + "textContent": "9", "type": [ "PublicationXref", "PubMed:16295699" @@ -39012,8 +39012,8 @@ "textContent": "Name: Pluripotent stem cell differentiation pathway\nLast Modified: 20240720120208\nOrganism: Homo sapiens", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0000004", - "http://identifiers.org/pw/PW:0000168" + "http://identifiers.org/pw/PW:0000168", + "http://identifiers.org/pw/PW:0000004" ], "verticalAlign": "top", "width": 1866.7010014306143, diff --git a/pathways/WP3529/WP3529.gpml b/pathways/WP3529/WP3529.gpml index a9b62cb30..b0b3f8b64 100644 --- a/pathways/WP3529/WP3529.gpml +++ b/pathways/WP3529/WP3529.gpml @@ -848,10 +848,22 @@ - mammary gland epithelial cell - CL:0002327 + neuron + CL:0000540 Cell Type + + type B pancreatic cell + CL:0000169 + Cell Type + + + 17344318 + PubMed + Role of GAC63 in transcriptional activation mediated by beta-catenin. + Chen YH; Yang CK; Xia M; Ou CY; Stallcup MR + 2007 + 24710731 PubMed @@ -862,29 +874,6 @@ Hashimoto A Fujimoto S. - - 10755665 - PubMed - Induction, regulation, degradation, and biological significance of mammalian metallothioneins. - Crit Rev Biochem Mol Biol - 2000 - Miles AT - Hawksworth GM - Beattie JH - Rodilla V - - - homeostasis pathway - PW:0000355 - Pathway Ontology - - - 22289350 - PubMed - The taste of heavy metals: gene regulation by MTF-1 - - 2012 - 23506888 PubMed @@ -894,26 +883,21 @@ Huang L Tepaamorndech S. - - 23506894 - PubMed - The SLC39 family of zinc transporters - Mol Aspects Med. 2013 - 2013 - Jeong J - Eide DJ - - type B pancreatic cell - CL:0000169 - Cell Type + homeostasis pathway + PW:0000355 + Pathway Ontology - - 17344318 + + 10755665 PubMed - Role of GAC63 in transcriptional activation mediated by beta-catenin. - Chen YH; Yang CK; Xia M; Ou CY; Stallcup MR - 2007 + Induction, regulation, degradation, and biological significance of mammalian metallothioneins + Crit Rev Biochem Mol Biol. 2000;35(1):35-70. + 2000 + Miles AT + Hawksworth GM + Beattie JH + Rodilla V. 22057392 @@ -922,11 +906,6 @@ 2012 - - neuron - CL:0000540 - Cell Type - 24416395 PubMed @@ -950,17 +929,38 @@ Adam V, Kizek R Masarik M. - + + 22289350 + PubMed + The taste of heavy metals: gene regulation by MTF-1 + + 2012 + + 10755665 PubMed - Induction, regulation, degradation, and biological significance of mammalian metallothioneins - Crit Rev Biochem Mol Biol. 2000;35(1):35-70. + Induction, regulation, degradation, and biological significance of mammalian metallothioneins. + Crit Rev Biochem Mol Biol 2000 Miles AT Hawksworth GM Beattie JH - Rodilla V. + Rodilla V + + 23506894 + PubMed + The SLC39 family of zinc transporters + Mol Aspects Med. 2013 + 2013 + Jeong J + Eide DJ + + + mammary gland epithelial cell + CL:0002327 + Cell Type + 11831458 PubMed diff --git a/pathways/WP3529/WP3529.json b/pathways/WP3529/WP3529.json index b42229c59..12ab95da5 100644 --- a/pathways/WP3529/WP3529.json +++ b/pathways/WP3529/WP3529.json @@ -8536,7 +8536,7 @@ "gpmlElementName": "PublicationXref", "id": "publicationXrefb6b", "standardName": "The taste of heavy metals: gene regulation by MTF-1", - "textContent": "5", + "textContent": "6", "type": [ "PublicationXref", "PubMed:22289350" @@ -8549,7 +8549,7 @@ "gpmlElementName": "PublicationXref", "id": "publicationXrefb85", "standardName": "A conserved cysteine cluster, essential for transcriptional activity, mediates homodimerization of human metal-responsive transcription factor-1 (MTF-1).", - "textContent": "6", + "textContent": "5", "type": [ "PublicationXref", "PubMed:22057392" @@ -8617,7 +8617,7 @@ "id": "publicationXrefd55", "source": "Crit Rev Biochem Mol Biol. 2000;35(1):35-70.", "standardName": "Induction, regulation, degradation, and biological significance of mammalian metallothioneins", - "textContent": "2", + "textContent": "1", "type": [ "PublicationXref", "PubMed:10755665" @@ -8657,7 +8657,7 @@ "id": "publicationXrefeaf", "source": "Crit Rev Biochem Mol Biol", "standardName": "Induction, regulation, degradation, and biological significance of mammalian metallothioneins.", - "textContent": "1", + "textContent": "2", "type": [ "PublicationXref", "PubMed:10755665" diff --git a/pathways/WP3622/WP3622.gpml b/pathways/WP3622/WP3622.gpml index 0f30ff847..11c89a6ec 100644 --- a/pathways/WP3622/WP3622.gpml +++ b/pathways/WP3622/WP3622.gpml @@ -1620,9 +1620,20 @@ + + 25342293 + PubMed + Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects. + Nat Prod Rep + 2015 + Sumner LW + Lei Z + Nikolau BJ + Saito K + - classic metabolic pathway - PW:0000002 + fatty acid biosynthetic pathway + PW:0000029 Pathway Ontology @@ -1639,6 +1650,16 @@ Fukushima A Kusano M + + glycolysis pathway + PW:0000640 + Pathway Ontology + + + flavonoid biosynthetic pathway + PW:0000522 + Pathway Ontology + 23473981 PubMed @@ -1654,18 +1675,8 @@ Fernie AR - glycolysis pathway - PW:0000640 - Pathway Ontology - - - fatty acid biosynthetic pathway - PW:0000029 - Pathway Ontology - - - flavonoid biosynthetic pathway - PW:0000522 + classic metabolic pathway + PW:0000002 Pathway Ontology @@ -1673,17 +1684,6 @@ PW:0000011 Pathway Ontology - - 25342293 - PubMed - Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects. - Nat Prod Rep - 2015 - Sumner LW - Lei Z - Nikolau BJ - Saito K - diff --git a/pathways/WP3622/WP3622.json b/pathways/WP3622/WP3622.json index 37c174e13..10072578b 100644 --- a/pathways/WP3622/WP3622.json +++ b/pathways/WP3622/WP3622.json @@ -15413,11 +15413,11 @@ "textContent": "Name: AtMetExpress overview\nLast Modified: 20240720112524\nOrganism: Arabidopsis thaliana", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0000002", + "http://identifiers.org/pw/PW:0000029", "http://identifiers.org/pw/PW:0000026", "http://identifiers.org/pw/PW:0000640", - "http://identifiers.org/pw/PW:0000029", "http://identifiers.org/pw/PW:0000522", + "http://identifiers.org/pw/PW:0000002", "http://identifiers.org/pw/PW:0000011" ], "verticalAlign": "top", diff --git a/pathways/WP3890/WP3890.gpml b/pathways/WP3890/WP3890.gpml index c2d5ed5b5..5fe6839c5 100644 --- a/pathways/WP3890/WP3890.gpml +++ b/pathways/WP3890/WP3890.gpml @@ -222,8 +222,13 @@ - nanomaterial response pathway - PW:0001435 + innate immune response pathway + PW:0000234 + Pathway Ontology + + + xenobiotic metabolic pathway + PW:0001229 Pathway Ontology @@ -236,13 +241,13 @@ Fadeel B - macrophage - CL:0000235 - Cell Type + nanomaterial response pathway + PW:0001435 + Pathway Ontology - innate immune response pathway - PW:0000234 + regulatory pathway + PW:0000004 Pathway Ontology @@ -257,14 +262,9 @@ Fadeel B - xenobiotic metabolic pathway - PW:0001229 - Pathway Ontology - - - regulatory pathway - PW:0000004 - Pathway Ontology + macrophage + CL:0000235 + Cell Type diff --git a/pathways/WP3890/WP3890.json b/pathways/WP3890/WP3890.json index d48c3d3b2..edcb99870 100644 --- a/pathways/WP3890/WP3890.json +++ b/pathways/WP3890/WP3890.json @@ -2242,9 +2242,9 @@ "textContent": "Name: Nanomaterial-induced inflammasome activation\nLast Modified: 20240720125102\nOrganism: Homo sapiens", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0001435", "http://identifiers.org/pw/PW:0000234", "http://identifiers.org/pw/PW:0001229", + "http://identifiers.org/pw/PW:0001435", "http://identifiers.org/pw/PW:0000004" ], "verticalAlign": "top", diff --git a/pathways/WP3896/WP3896.gpml b/pathways/WP3896/WP3896.gpml index c933866d8..5f2e77d50 100644 --- a/pathways/WP3896/WP3896.gpml +++ b/pathways/WP3896/WP3896.gpml @@ -1082,13 +1082,23 @@ Source: KEGG (http://www.genome.jp/dbget-bin/www_bget?pathway:map04610) - infectious disease pathway - PW:0001028 + coagulation cascade pathway + PW:0000474 Pathway Ontology - coagulation cascade pathway - PW:0000474 + dengue disease + DOID:12205 + Disease + + + complement system pathway + PW:0000502 + Pathway Ontology + + + infectious disease pathway + PW:0001028 Pathway Ontology @@ -1107,16 +1117,6 @@ Source: KEGG (http://www.genome.jp/dbget-bin/www_bget?pathway:map04610)Fathman CG Soares LR - - dengue disease - DOID:12205 - Disease - - - complement system pathway - PW:0000502 - Pathway Ontology - diff --git a/pathways/WP3896/WP3896.json b/pathways/WP3896/WP3896.json index 20479fccd..19a5dde1a 100644 --- a/pathways/WP3896/WP3896.json +++ b/pathways/WP3896/WP3896.json @@ -10685,10 +10685,10 @@ "textContent": "Name: Dengue-2 interactions with complement and coagulation cascades\nLast Modified: 20240720052349\nOrganism: Homo sapiens", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0001028", "http://identifiers.org/pw/PW:0000474", - "http://identifiers.org/pw/PW:0000526", - "http://identifiers.org/pw/PW:0000502" + "http://identifiers.org/pw/PW:0000502", + "http://identifiers.org/pw/PW:0001028", + "http://identifiers.org/pw/PW:0000526" ], "verticalAlign": "top", "width": 1158.6666666666665, diff --git a/pathways/WP3915/WP3915.gpml b/pathways/WP3915/WP3915.gpml index 7b261678a..aa0a8df11 100644 --- a/pathways/WP3915/WP3915.gpml +++ b/pathways/WP3915/WP3915.gpml @@ -1971,49 +1971,147 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - 10692429 + + 15581595 PubMed - Dynamics of protein-tyrosine phosphatases in rat adipocytes. - J Biol Chem - 2000 - Calera MR - Vallega G - Pilch PF + Regulatory network of lipid-sensing nuclear receptors: roles for CAR, PXR, LXR, and FXR. + Arch Biochem Biophys + 2005 + Handschin C + Meyer UA - - 21440577 + + 16244323 PubMed - Interplay between FOXO, TOR, and Akt. - Biochim Biophys Acta - 2011 - Hay N + Tuberous sclerosis: a GAP at the crossroads of multiple signaling pathways. + Hum Mol Genet + 2005 + Kwiatkowski DJ + Manning BD - - 23150577 + + 26235620 PubMed - Atypical angiopoietin-like protein that regulates ANGPTL3. - Proc Natl Acad Sci U S A - 2012 - Quagliarini F + A Positive Feedback Loop between Akt and mTORC2 via SIN1 Phosphorylation. + Cell Rep + 2015 + Yang G + Murashige DS + Humphrey SJ + James DE + + + 11282018 + PubMed + Insulin signalling. + J Cell Sci + 2001 + Bevan P + + + angiopoietin signaling pathway + PW:0000489 + Pathway Ontology + + + 9228007 + PubMed + Dual role of phosphatidylinositol-3,4,5-trisphosphate in the activation of protein kinase B. + Science + 1997 + Stokoe D + Stephens LR + Copeland T + Gaffney PR + Reese CB + Painter GF + Holmes AB + McCormick F + Hawkins PT + + + 26254015 + PubMed + AMP-activated protein kinase suppresses the expression of LXR/SREBP-1 signaling-induced ANGPTL8 in HepG2 cells. + Mol Cell Endocrinol + 2015 + Lee J + Hong SW + Park SE + Rhee EJ + Park CY + Oh KW + Park SW + Lee WY + + + 23516131 + PubMed + A pathway approach to investigate the function and regulation of SREBPs. + Genes Nutr + 2013 + Daemen S + Kutmon M + Evelo CT + + + 9094314 + PubMed + Characterization of a 3-phosphoinositide-dependent protein kinase which phosphorylates and activates protein kinase Balpha. + Curr Biol + 1997 + Alessi DR + James SR + Downes CP + Holmes AB + Gaffney PR + Reese CB + Cohen P + + + hepatocyte + CL:0000182 + Cell Type + + + 23261442 + PubMed + Lipasin, thermoregulated in brown fat, is a novel but atypical member of the angiopoietin-like protein family. + Biochem Biophys Res Commun + 2013 + Fu Z + Yao F + Abou-Samra AB + Zhang R + + + 26490400 + PubMed + Transcriptional regulation of hepatic lipogenesis. + Nat Rev Mol Cell Biol + 2015 Wang Y - Kozlitina J - Grishin NV - Hyde R - Boerwinkle E - Valenzuela DM - Murphy AJ - Cohen JC - Hobbs HH + Viscarra J + Kim SJ + Sul HS - - 21908933 + + 15610735 PubMed - Crosstalk of thyroid hormone receptor and liver X receptor in lipid metabolism and beyond [Review]. - Endocr J - 2011 - Hashimoto K - Mori M + A structural basis for constitutive activity in the human CAR/RXRalpha heterodimer. + Mol Cell + 2004 + Xu RX + Lambert MH + Wisely BB + Warren EN + Weinert EE + Waitt GM + Williams JD + Collins JL + Moore LB + Willson TM + Moore JT 20412774 @@ -2030,26 +2128,28 @@ Proteins on this pathway have targeted assays available via the [https://assays. Park Y Hay N + + 10692429 + PubMed + Dynamics of protein-tyrosine phosphatases in rat adipocytes. + J Biol Chem + 2000 + Calera MR + Vallega G + Pilch PF + - angiopoietin signaling pathway - PW:0000489 + insulin signaling pathway + PW:0000143 Pathway Ontology - - 19158095 + + 21440577 PubMed - Insulin enhances post-translational processing of nascent SREBP-1c by promoting its phosphorylation and association with COPII vesicles. - J Biol Chem - 2009 - Yellaturu CR - Deng X - Cagen LM - Wilcox HG - Mansbach CM 2nd - Siddiqi SA - Park EA - Raghow R - Elam MB + Interplay between FOXO, TOR, and Akt. + Biochim Biophys Acta + 2011 + Hay N 26387753 @@ -2072,100 +2172,49 @@ Proteins on this pathway have targeted assays available via the [https://assays. Jiao Bian L Sheng Li D - - 11282018 - PubMed - Insulin signalling. - J Cell Sci - 2001 - Bevan P - - - 24379912 + + 20117946 PubMed - Betatrophin: A liver-derived hormone for the pancreatic β-cell proliferation. - World J Diabetes - 2013 - Raghow R + The Akt-SREBP nexus: cell signaling meets lipid metabolism. + Trends Endocrinol Metab + 2010 + Krycer JR + Sharpe LJ + Luu W + Brown AJ - - 21453770 + + 26569053 PubMed - Cross-regulation of hepatic glucose metabolism via ChREBP and nuclear receptors. + Angiopoietin-like protein 8 (betatrophin) is a stress-response protein that down-regulates expression of adipocyte triglyceride lipase. Biochim Biophys Acta - 2011 - Poupeau A - Postic C + 2016 + Zhang Y + Li S + Donelan W + Xie C + Wang H + Wu Q + Purich DL + Reeves WH + Tang D + Yang LJ - - 25720603 + + 19158095 PubMed - In vivo targeted delivery of ANGPTL8 gene for beta cell regeneration in rats. - Diabetologia - 2015 - Chen J - Chen S - Huang P - Meng XL - Clayton S - Shen JS - Grayburn PA - - - 23802099 - PubMed - The Paradox of Akt-mTOR Interactions. - Front Oncol - 2013 - Vadlakonda L - Dash A - Pasupuleti M - Anil Kumar K - Reddanna P - - - hepatocyte - CL:0000182 - Cell Type - - - 16916938 - PubMed - The reciprocal stability of FOXO1 and IRS2 creates a regulatory circuit that controls insulin signaling. - Mol Endocrinol - 2006 - Guo S - Dunn SL - White MF - - - 8826975 - PubMed - - - - - - insulin signaling pathway - PW:0000143 - Pathway Ontology - - - 26499800 - PubMed - Coupling between Nutrient Availability and Thyroid Hormone Activation - - 2015 - 26499800 - PubMed - Coupling between Nutrient Availability and Thyroid Hormone Activation - - 2015 - Lartey LJ - Werneck-de-Castro JP - O-Sullivan I - Unterman TG - Bianco AC + Insulin enhances post-translational processing of nascent SREBP-1c by promoting its phosphorylation and association with COPII vesicles. + J Biol Chem + 2009 + Yellaturu CR + Deng X + Cagen LM + Wilcox HG + Mansbach CM 2nd + Siddiqi SA + Park EA + Raghow R + Elam MB 11875109 @@ -2182,6 +2231,32 @@ Proteins on this pathway have targeted assays available via the [https://assays. Xia C Lala DS + + 23150577 + PubMed + Atypical angiopoietin-like protein that regulates ANGPTL3. + Proc Natl Acad Sci U S A + 2012 + Quagliarini F + Wang Y + Kozlitina J + Grishin NV + Hyde R + Boerwinkle E + Valenzuela DM + Murphy AJ + Cohen JC + Hobbs HH + + + 21453770 + PubMed + Cross-regulation of hepatic glucose metabolism via ChREBP and nuclear receptors. + Biochim Biophys Acta + 2011 + Poupeau A + Postic C + 20698033 PubMed @@ -2193,196 +2268,78 @@ Proteins on this pathway have targeted assays available via the [https://assays. Kim YJ Kim SG - - 21908933 - PubMed - Crosstalk of thyroid hormone receptor and liver X receptor in lipid metabolism and beyond [Review]. - Endocr J - 2011 - Hashimoto K - Mori M - - - 8702689 - PubMed - Protein-tyrosine phosphatase 1B is a negative regulator of insulin- and insulin-like growth factor-I-stimulated signaling. - J Biol Chem - 1996 - Kenner KA - Anyanwu E - Olefsky JM - Kusari J - - - 26235620 - PubMed - A Positive Feedback Loop between Akt and mTORC2 via SIN1 Phosphorylation. - Cell Rep - 2015 - Yang G - Murashige DS - Humphrey SJ - James DE - - - 19683471 - PubMed - Cellular mechanisms of insulin resistance: role of stress-regulated serine kinases and insulin receptor substrates (IRS) serine phosphorylation. - Curr Opin Pharmacol - 2009 - Tanti JF - Jager J - - - 27410263 + + 22569073 PubMed - Resolving Discrepant Findings on ANGPTL8 in β-Cell Proliferation: A Collaborative Approach to Resolving the Betatrophin Controversy. - PLoS One - 2016 - Cox AR - Barrandon O - Cai EP - Rios JS - Chavez J - Bonnyman CW - Lam CJ - Yi P - Melton DA - Kushner JA + Identification of RIFL, a novel adipocyte-enriched insulin target gene with a role in lipid metabolism. + Am J Physiol Endocrinol Metab + 2012 + Ren G + Kim JY + Smas CM - - 24852694 + + 24379912 PubMed - Elevated circulating lipasin/betatrophin in human type 2 diabetes and obesity. - Sci Rep - 2014 - Fu Z - Berhane F - Fite A - Seyoum B - Abou-Samra AB - Zhang R + Betatrophin: A liver-derived hormone for the pancreatic β-cell proliferation. + World J Diabetes + 2013 + Raghow R regulatory pathway PW:0000004 Pathway Ontology - - 23516131 - PubMed - A pathway approach to investigate the function and regulation of SREBPs. - Genes Nutr - 2013 - Daemen S - Kutmon M - Evelo CT - - - 26254015 - PubMed - AMP-activated protein kinase suppresses the expression of LXR/SREBP-1 signaling-induced ANGPTL8 in HepG2 cells. - Mol Cell Endocrinol - 2015 - Lee J - Hong SW - Park SE - Rhee EJ - Park CY - Oh KW - Park SW - Lee WY - - - 9094314 - PubMed - Characterization of a 3-phosphoinositide-dependent protein kinase which phosphorylates and activates protein kinase Balpha. - Curr Biol - 1997 - Alessi DR - James SR - Downes CP - Holmes AB - Gaffney PR - Reese CB - Cohen P - - - 21310851 - PubMed - MicroRNA hsa-miR-613 targets the human LXRα gene and mediates a feedback loop of LXRα autoregulation. - Mol Endocrinol - 2011 - Ou Z - Wada T - Gramignoli R - Li S - Strom SC - Huang M - Xie W - - - 9228007 - PubMed - Dual role of phosphatidylinositol-3,4,5-trisphosphate in the activation of protein kinase B. - Science - 1997 - Stokoe D - Stephens LR - Copeland T - Gaffney PR - Reese CB - Painter GF - Holmes AB - McCormick F - Hawkins PT - - - 15581595 + + 8826975 PubMed - Regulatory network of lipid-sensing nuclear receptors: roles for CAR, PXR, LXR, and FXR. - Arch Biochem Biophys - 2005 - Handschin C - Meyer UA + + + - - 26569053 + + 23802099 PubMed - Angiopoietin-like protein 8 (betatrophin) is a stress-response protein that down-regulates expression of adipocyte triglyceride lipase. - Biochim Biophys Acta - 2016 - Zhang Y - Li S - Donelan W - Xie C - Wang H - Wu Q - Purich DL - Reeves WH - Tang D - Yang LJ + The Paradox of Akt-mTOR Interactions. + Front Oncol + 2013 + Vadlakonda L + Dash A + Pasupuleti M + Anil Kumar K + Reddanna P - - 17234883 + + 26499800 PubMed - IRES-mediated functional coupling of transcription and translation amplifies insulin receptor feedback. - Genes Dev - 2007 - Marr MT 2nd - D'Alessio JA - Puig O - Tjian R + Coupling between Nutrient Availability and Thyroid Hormone Activation + + 2015 + 26499800 + PubMed + Coupling between Nutrient Availability and Thyroid Hormone Activation + + 2015 + Lartey LJ + Werneck-de-Castro JP + O-Sullivan I + Unterman TG + Bianco AC - - 16493415 + + 21310851 PubMed - Critical nodes in signalling pathways: insights into insulin action. - Nat Rev Mol Cell Biol - 2006 - Taniguchi CM - Emanuelli B - Kahn CR + MicroRNA hsa-miR-613 targets the human LXRα gene and mediates a feedback loop of LXRα autoregulation. + Mol Endocrinol + 2011 + Ou Z + Wada T + Gramignoli R + Li S + Strom SC + Huang M + Xie W 22927400 @@ -2399,47 +2356,25 @@ Proteins on this pathway have targeted assays available via the [https://assays. Goldstein JL Brown MS - - 23261442 - PubMed - Lipasin, thermoregulated in brown fat, is a novel but atypical member of the angiopoietin-like protein family. - Biochem Biophys Res Commun - 2013 - Fu Z - Yao F - Abou-Samra AB - Zhang R - - - 20117946 - PubMed - The Akt-SREBP nexus: cell signaling meets lipid metabolism. - Trends Endocrinol Metab - 2010 - Krycer JR - Sharpe LJ - Luu W - Brown AJ - - - 26490400 + + 21908933 PubMed - Transcriptional regulation of hepatic lipogenesis. - Nat Rev Mol Cell Biol - 2015 - Wang Y - Viscarra J - Kim SJ - Sul HS + Crosstalk of thyroid hormone receptor and liver X receptor in lipid metabolism and beyond [Review]. + Endocr J + 2011 + Hashimoto K + Mori M - - 11742412 + + 8702689 PubMed - Insulin signalling and the regulation of glucose and lipid metabolism. - Nature - 2001 - Saltiel AR - Kahn CR + Protein-tyrosine phosphatase 1B is a negative regulator of insulin- and insulin-like growth factor-I-stimulated signaling. + J Biol Chem + 1996 + Kenner KA + Anyanwu E + Olefsky JM + Kusari J 24262987 @@ -2462,39 +2397,6 @@ Proteins on this pathway have targeted assays available via the [https://assays. Lin YH Lin KH - - 19324998 - PubMed - Carbohydrate response element binding protein gene expression is positively regulated by thyroid hormone. - Endocrinology - 2009 - Hashimoto K - Ishida E - Matsumoto S - Okada S - Yamada M - Satoh T - Monden T - Mori M - - - 15610735 - PubMed - A structural basis for constitutive activity in the human CAR/RXRalpha heterodimer. - Mol Cell - 2004 - Xu RX - Lambert MH - Wisely BB - Warren EN - Weinert EE - Waitt GM - Williams JD - Collins JL - Moore LB - Willson TM - Moore JT - 11803135 PubMed @@ -2508,24 +2410,122 @@ Proteins on this pathway have targeted assays available via the [https://assays. French SW Wan YJ - - 22569073 + + 19683471 PubMed - Identification of RIFL, a novel adipocyte-enriched insulin target gene with a role in lipid metabolism. - Am J Physiol Endocrinol Metab - 2012 - Ren G - Kim JY - Smas CM + Cellular mechanisms of insulin resistance: role of stress-regulated serine kinases and insulin receptor substrates (IRS) serine phosphorylation. + Curr Opin Pharmacol + 2009 + Tanti JF + Jager J - - 16244323 + + 24852694 PubMed - Tuberous sclerosis: a GAP at the crossroads of multiple signaling pathways. - Hum Mol Genet - 2005 - Kwiatkowski DJ - Manning BD + Elevated circulating lipasin/betatrophin in human type 2 diabetes and obesity. + Sci Rep + 2014 + Fu Z + Berhane F + Fite A + Seyoum B + Abou-Samra AB + Zhang R + + + 16493415 + PubMed + Critical nodes in signalling pathways: insights into insulin action. + Nat Rev Mol Cell Biol + 2006 + Taniguchi CM + Emanuelli B + Kahn CR + + + 11742412 + PubMed + Insulin signalling and the regulation of glucose and lipid metabolism. + Nature + 2001 + Saltiel AR + Kahn CR + + + 17234883 + PubMed + IRES-mediated functional coupling of transcription and translation amplifies insulin receptor feedback. + Genes Dev + 2007 + Marr MT 2nd + D'Alessio JA + Puig O + Tjian R + + + 25720603 + PubMed + In vivo targeted delivery of ANGPTL8 gene for beta cell regeneration in rats. + Diabetologia + 2015 + Chen J + Chen S + Huang P + Meng XL + Clayton S + Shen JS + Grayburn PA + + + 16916938 + PubMed + The reciprocal stability of FOXO1 and IRS2 creates a regulatory circuit that controls insulin signaling. + Mol Endocrinol + 2006 + Guo S + Dunn SL + White MF + + + 21908933 + PubMed + Crosstalk of thyroid hormone receptor and liver X receptor in lipid metabolism and beyond [Review]. + Endocr J + 2011 + Hashimoto K + Mori M + + + 27410263 + PubMed + Resolving Discrepant Findings on ANGPTL8 in β-Cell Proliferation: A Collaborative Approach to Resolving the Betatrophin Controversy. + PLoS One + 2016 + Cox AR + Barrandon O + Cai EP + Rios JS + Chavez J + Bonnyman CW + Lam CJ + Yi P + Melton DA + Kushner JA + + + 19324998 + PubMed + Carbohydrate response element binding protein gene expression is positively regulated by thyroid hormone. + Endocrinology + 2009 + Hashimoto K + Ishida E + Matsumoto S + Okada S + Yamada M + Satoh T + Monden T + Mori M diff --git a/pathways/WP3915/WP3915.json b/pathways/WP3915/WP3915.json index 4fdefdb97..fa4b3e5d5 100644 --- a/pathways/WP3915/WP3915.json +++ b/pathways/WP3915/WP3915.json @@ -18376,7 +18376,7 @@ "id": "publicationXrefa23", "source": "Diabetologia", "standardName": "In vivo targeted delivery of ANGPTL8 gene for beta cell regeneration in rats.", - "textContent": "35", + "textContent": "39", "type": [ "PublicationXref", "PubMed:25720603" @@ -18400,7 +18400,7 @@ "id": "publicationXrefa63", "source": "Proc Natl Acad Sci U S A", "standardName": "Insulin stimulation of SREBP-1c processing in transgenic rat hepatocytes requires p70 S6-kinase.", - "textContent": "27", + "textContent": "28", "type": [ "PublicationXref", "PubMed:22927400" @@ -18420,7 +18420,7 @@ "id": "publicationXrefaa3", "source": "Nat Rev Mol Cell Biol", "standardName": "Transcriptional regulation of hepatic lipogenesis.", - "textContent": "41", + "textContent": "37", "type": [ "PublicationXref", "PubMed:26490400" @@ -18445,7 +18445,7 @@ "id": "publicationXrefab8", "source": "Exp Cell Res", "standardName": "ANGPTL8/betatrophin alleviates insulin resistance via the Akt-GSK3β or Akt-FoxO1 pathway in HepG2 cells.", - "textContent": "36", + "textContent": "40", "type": [ "PublicationXref", "PubMed:26387753" @@ -18462,7 +18462,7 @@ "id": "publicationXrefac5", "source": "World J Diabetes", "standardName": "Betatrophin: A liver-derived hormone for the pancreatic β-cell proliferation.", - "textContent": "29", + "textContent": "31", "type": [ "PublicationXref", "PubMed:24379912" @@ -18483,7 +18483,7 @@ "id": "publicationXrefad5", "source": "Front Oncol", "standardName": "The Paradox of Akt-mTOR Interactions.", - "textContent": "30", + "textContent": "32", "type": [ "PublicationXref", "PubMed:23802099" @@ -18509,7 +18509,7 @@ "id": "publicationXrefaed", "source": "Biochim Biophys Acta", "standardName": "Angiopoietin-like protein 8 (betatrophin) is a stress-response protein that down-regulates expression of adipocyte triglyceride lipase.", - "textContent": "43", + "textContent": "41", "type": [ "PublicationXref", "PubMed:26569053" @@ -18529,7 +18529,7 @@ "id": "publicationXrefb0e", "source": "Trends Endocrinol Metab", "standardName": "The Akt-SREBP nexus: cell signaling meets lipid metabolism.", - "textContent": "20", + "textContent": "19", "type": [ "PublicationXref", "PubMed:20117946" @@ -18572,7 +18572,7 @@ "id": "publicationXrefb8b", "source": "Autophagy", "standardName": "Chromosome 19 open reading frame 80 is upregulated by thyroid hormone and modulates autophagy and lipid metabolism.", - "textContent": "34", + "textContent": "33", "type": [ "PublicationXref", "PubMed:24262987" @@ -18595,7 +18595,7 @@ "id": "publicationXrefba9", "source": "Curr Biol", "standardName": "Characterization of a 3-phosphoinositide-dependent protein kinase which phosphorylates and activates protein kinase Balpha.", - "textContent": "2", + "textContent": "3", "type": [ "PublicationXref", "PubMed:9094314" @@ -18631,7 +18631,7 @@ "publicationXrefbdc": { "gpmlElementName": "PublicationXref", "id": "publicationXrefbdc", - "textContent": "37", + "textContent": "42", "type": [ "PublicationXref", "PubMed:8826975" @@ -18696,7 +18696,7 @@ "id": "publicationXrefc37", "source": "Nat Rev Mol Cell Biol", "standardName": "Critical nodes in signalling pathways: insights into insulin action.", - "textContent": "13", + "textContent": "12", "type": [ "PublicationXref", "PubMed:16493415" @@ -18858,7 +18858,7 @@ "id": "publicationXrefd5a", "source": "Genes Nutr", "standardName": "A pathway approach to investigate the function and regulation of SREBPs.", - "textContent": "31", + "textContent": "29", "type": [ "PublicationXref", "PubMed:23516131" @@ -18878,7 +18878,7 @@ "id": "publicationXrefd7b", "source": "Cell Rep", "standardName": "A Positive Feedback Loop between Akt and mTORC2 via SIN1 Phosphorylation.", - "textContent": "39", + "textContent": "35", "type": [ "PublicationXref", "PubMed:26235620" @@ -18902,7 +18902,7 @@ "id": "publicationXrefd9b", "source": "Mol Cell Endocrinol", "standardName": "AMP-activated protein kinase suppresses the expression of LXR/SREBP-1 signaling-induced ANGPTL8 in HepG2 cells.", - "textContent": "40", + "textContent": "36", "type": [ "PublicationXref", "PubMed:26254015" @@ -18963,7 +18963,7 @@ "id": "publicationXrefe1a", "source": "Am J Physiol Endocrinol Metab", "standardName": "Identification of RIFL, a novel adipocyte-enriched insulin target gene with a role in lipid metabolism.", - "textContent": "28", + "textContent": "27", "type": [ "PublicationXref", "PubMed:22569073" @@ -18983,7 +18983,7 @@ "id": "publicationXrefe2e", "source": "World J Gastroenterol", "standardName": "AMPK-associated signaling to bridge the gap between fuel metabolism and hepatocyte viability.", - "textContent": "19", + "textContent": "20", "type": [ "PublicationXref", "PubMed:20698033" @@ -19045,7 +19045,7 @@ "id": "publicationXrefea1", "source": "Biochem Biophys Res Commun", "standardName": "Lipasin, thermoregulated in brown fat, is a novel but atypical member of the angiopoietin-like protein family.", - "textContent": "32", + "textContent": "30", "type": [ "PublicationXref", "PubMed:23261442" @@ -19063,7 +19063,7 @@ "id": "publicationXrefec9", "source": "Endocr J", "standardName": "Crosstalk of thyroid hormone receptor and liver X receptor in lipid metabolism and beyond [Review].", - "textContent": "22", + "textContent": "25", "type": [ "PublicationXref", "PubMed:21908933" @@ -19103,7 +19103,7 @@ "id": "publicationXrefef4", "source": "Sci Rep", "standardName": "Elevated circulating lipasin/betatrophin in human type 2 diabetes and obesity.", - "textContent": "33", + "textContent": "34", "type": [ "PublicationXref", "PubMed:24852694" @@ -19121,7 +19121,7 @@ "id": "publicationXreff18", "source": "Biochim Biophys Acta", "standardName": "Cross-regulation of hepatic glucose metabolism via ChREBP and nuclear receptors.", - "textContent": "23", + "textContent": "22", "type": [ "PublicationXref", "PubMed:21453770" @@ -19163,7 +19163,7 @@ "id": "publicationXreff32", "source": "Science", "standardName": "Dual role of phosphatidylinositol-3,4,5-trisphosphate in the activation of protein kinase B.", - "textContent": "3", + "textContent": "2", "type": [ "PublicationXref", "PubMed:9228007" @@ -19210,7 +19210,7 @@ "id": "publicationXreff5e", "source": "Mol Endocrinol", "standardName": "MicroRNA hsa-miR-613 targets the human LXRα gene and mediates a feedback loop of LXRα autoregulation.", - "textContent": "25", + "textContent": "23", "type": [ "PublicationXref", "PubMed:21310851" @@ -19236,7 +19236,7 @@ "id": "publicationXreffba", "source": "PLoS One", "standardName": "Resolving Discrepant Findings on ANGPTL8 in β-Cell Proliferation: A Collaborative Approach to Resolving the Betatrophin Controversy.", - "textContent": "42", + "textContent": "43", "type": [ "PublicationXref", "PubMed:27410263" @@ -19255,7 +19255,7 @@ "id": "publicationXrefff9", "source": "Mol Endocrinol", "standardName": "The reciprocal stability of FOXO1 and IRS2 creates a regulatory circuit that controls insulin signaling.", - "textContent": "12", + "textContent": "13", "type": [ "PublicationXref", "PubMed:16916938" diff --git a/pathways/WP3931/WP3931.gpml b/pathways/WP3931/WP3931.gpml index 485db7bd5..d9ce74418 100644 --- a/pathways/WP3931/WP3931.gpml +++ b/pathways/WP3931/WP3931.gpml @@ -1466,6 +1466,31 @@ Proteins on this pathway have targeted assays available via the [https://assays. + + 18220859 + PubMed + Intracellular signaling pathways regulating pluripotency of embryonic stem cells. + Curr Stem Cell Res Ther + 2006 + Okita K + Yamanaka S + + + 18682835 + PubMed + Dorsomorphin, a selective small molecule inhibitor of BMP signaling, promotes cardiomyogenesis in embryonic stem cells. + PLoS ONE + 2008 + Hao J + Daleo MA + Murphy CK + Yu PB + Ho JN + Hu J + Peterson RT + Hatzopoulos AK + Hong CC + 15867910 PubMed @@ -1485,6 +1510,11 @@ Proteins on this pathway have targeted assays available via the [https://assays. Okano H Fukuda K + + embryonic stem cell + CL:0002322 + Cell Type + 11602624 PubMed @@ -1511,41 +1541,11 @@ Proteins on this pathway have targeted assays available via the [https://assays. CL:0002322 Cell Type - - embryonic stem cell - CL:0002322 - Cell Type - - - 18220859 - PubMed - Intracellular signaling pathways regulating pluripotency of embryonic stem cells. - Curr Stem Cell Res Ther - 2006 - Okita K - Yamanaka S - the extracellular signal-regulated Raf/Mek/Erk signaling pathway PW:0000102 Pathway Ontology - - 18682835 - PubMed - Dorsomorphin, a selective small molecule inhibitor of BMP signaling, promotes cardiomyogenesis in embryonic stem cells. - PLoS ONE - 2008 - Hao J - Daleo MA - Murphy CK - Yu PB - Ho JN - Hu J - Peterson RT - Hatzopoulos AK - Hong CC - diff --git a/pathways/WP4216/WP4216.gpml b/pathways/WP4216/WP4216.gpml index 5cf735125..4269ea3b0 100644 --- a/pathways/WP4216/WP4216.gpml +++ b/pathways/WP4216/WP4216.gpml @@ -1005,11 +1005,6 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - epithelial cell - CL:0000066 - Cell Type - 25236910 PubMed @@ -1019,6 +1014,24 @@ Proteins on this pathway have targeted assays available via the [https://assays. Mazzoni SM Fearon ER + + 25736321 + PubMed + Transforming Growth Factor β Signaling in Colorectal Cancer Cells With Microsatellite Instability Despite Biallelic Mutations in TGFBR2. + Gastroenterology + 2015 + de Miranda NF + van Dinther M + van den Akker BE + van Wezel T + ten Dijke P + Morreau H + + + epithelial cell + CL:0000066 + Cell Type + 10479724 PubMed @@ -1031,39 +1044,25 @@ Proteins on this pathway have targeted assays available via the [https://assays. Emi M Moriyama Y - - 25514926 + + 18316791 PubMed - PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. - Nucleic Acids Res - 2015 - Hornbeck PV - Zhang B - Murray B - Kornhauser JM - Latham V - Skrzypek E + Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. + J Clin Oncol + 2008 + Amado RG + Wolf M + Peeters M + Van Cutsem E + Siena S + Freeman DJ + Juan T + Sikorski R + Suggs S + Radinsky R + Patterson SD + Chang DD - - colorectal cancer - DOID:9256 - Disease - - - cancer pathway - PW:0000605 - Pathway Ontology - - - altered DNA repair pathway - PW:0000292 - Pathway Ontology - - - colorectal cancer pathway - PW:0000612 - Pathway Ontology - 12821112 PubMed @@ -1073,7 +1072,31 @@ Proteins on this pathway have targeted assays available via the [https://assays. Miyaki M Kuroki T - + + colorectal cancer pathway + PW:0000612 + Pathway Ontology + + + 18316791 + PubMed + Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. + J Clin Oncol + 2008 + Amado RG + Wolf M + Peeters M + Van Cutsem E + Siena S + Freeman DJ + Juan T + Sikorski R + Suggs S + Radinsky R + Patterson SD + Chang DD + + 19679400 PubMed Frequency and type of KRAS mutations in routine diagnostic analysis of metastatic colorectal cancer. @@ -1089,25 +1112,6 @@ Proteins on this pathway have targeted assays available via the [https://assays. PW:0000598 Pathway Ontology - - 20420946 - PubMed - The chromosomal instability pathway in colon cancer. - Gastroenterology - 2010 - Pino MS - Chung DC - - - 14715079 - PubMed - Molecular and functional consequences of Smad4 C-terminal missense mutations in colorectal tumour cells. - Biochem J - 2004 - De Bosscher K - Hill CS - Nicolás FJ - 8898652 PubMed @@ -1122,58 +1126,7 @@ Proteins on this pathway have targeted assays available via the [https://assays. Shimokawa K Saji S - - 25736321 - PubMed - Transforming Growth Factor β Signaling in Colorectal Cancer Cells With Microsatellite Instability Despite Biallelic Mutations in TGFBR2. - Gastroenterology - 2015 - de Miranda NF - van Dinther M - van den Akker BE - van Wezel T - ten Dijke P - Morreau H - - - 18316791 - PubMed - Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. - J Clin Oncol - 2008 - Amado RG - Wolf M - Peeters M - Van Cutsem E - Siena S - Freeman DJ - Juan T - Sikorski R - Suggs S - Radinsky R - Patterson SD - Chang DD - - - 18316791 - PubMed - Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. - J Clin Oncol - 2008 - Amado RG - Wolf M - Peeters M - Van Cutsem E - Siena S - Freeman DJ - Juan T - Sikorski R - Suggs S - Radinsky R - Patterson SD - Chang DD - - + 19679400 PubMed Frequency and type of KRAS mutations in routine diagnostic analysis of metastatic colorectal cancer. @@ -1184,6 +1137,53 @@ Proteins on this pathway have targeted assays available via the [https://assays. Kirchner T Jung A + + 14715079 + PubMed + Molecular and functional consequences of Smad4 C-terminal missense mutations in colorectal tumour cells. + Biochem J + 2004 + De Bosscher K + Hill CS + Nicolás FJ + + + 25514926 + PubMed + PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. + Nucleic Acids Res + 2015 + Hornbeck PV + Zhang B + Murray B + Kornhauser JM + Latham V + Skrzypek E + + + colorectal cancer + DOID:9256 + Disease + + + 20420946 + PubMed + The chromosomal instability pathway in colon cancer. + Gastroenterology + 2010 + Pino MS + Chung DC + + + altered DNA repair pathway + PW:0000292 + Pathway Ontology + + + cancer pathway + PW:0000605 + Pathway Ontology + diff --git a/pathways/WP4216/WP4216.json b/pathways/WP4216/WP4216.json index ca6844be5..0eef2cb0b 100644 --- a/pathways/WP4216/WP4216.json +++ b/pathways/WP4216/WP4216.json @@ -10139,7 +10139,7 @@ "id": "publicationXrefaa2", "source": "Pathol Res Pract", "standardName": "Frequency and type of KRAS mutations in routine diagnostic analysis of metastatic colorectal cancer.", - "textContent": "8", + "textContent": "7", "type": [ "PublicationXref", "PubMed:19679400" @@ -10161,7 +10161,7 @@ "id": "publicationXrefbad", "source": "Gastroenterology", "standardName": "Transforming Growth Factor β Signaling in Colorectal Cancer Cells With Microsatellite Instability Despite Biallelic Mutations in TGFBR2.", - "textContent": "12", + "textContent": "11", "type": [ "PublicationXref", "PubMed:25736321" @@ -10183,7 +10183,7 @@ "id": "publicationXrefbd7", "source": "Nucleic Acids Res", "standardName": "PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.", - "textContent": "11", + "textContent": "12", "type": [ "PublicationXref", "PubMed:25514926" @@ -10229,7 +10229,7 @@ "id": "publicationXrefd1e", "source": "J Clin Oncol", "standardName": "Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer.", - "textContent": "5", + "textContent": "6", "type": [ "PublicationXref", "PubMed:18316791" @@ -10249,7 +10249,7 @@ "id": "publicationXrefd92", "source": "Pathol Res Pract", "standardName": "Frequency and type of KRAS mutations in routine diagnostic analysis of metastatic colorectal cancer.", - "textContent": "7", + "textContent": "8", "type": [ "PublicationXref", "PubMed:19679400" @@ -10277,7 +10277,7 @@ "id": "publicationXrefdaf", "source": "J Clin Oncol", "standardName": "Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer.", - "textContent": "6", + "textContent": "5", "type": [ "PublicationXref", "PubMed:18316791" @@ -10572,10 +10572,10 @@ "textContent": "Name: Chromosomal and microsatellite instability in colorectal cancer\nLast Modified: 20240720053605\nOrganism: Homo sapiens", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0000605", - "http://identifiers.org/pw/PW:0000292", "http://identifiers.org/pw/PW:0000612", - "http://identifiers.org/pw/PW:0000598" + "http://identifiers.org/pw/PW:0000598", + "http://identifiers.org/pw/PW:0000292", + "http://identifiers.org/pw/PW:0000605" ], "verticalAlign": "top", "width": 1611.2324929971987, diff --git a/pathways/WP4217/WP4217.gpml b/pathways/WP4217/WP4217.gpml index 000eeb472..1e9e7f550 100644 --- a/pathways/WP4217/WP4217.gpml +++ b/pathways/WP4217/WP4217.gpml @@ -1944,45 +1944,30 @@ This pathway was built using a text-mining approach to obtain interactions betwe - - 23573288 + + 16051304 PubMed - Lectin-dependent enhancement of Ebola virus infection via soluble and transmembrane C-type lectin receptors. - PLoS One - 2013 - Brudner M - Karpel M - Lear C - Chen L - Yantosca LM - Scully C - Sarraju A - Sokolovska A - Zariffard MR - Eisen DP - Mungall BA - Kotton DN - Omari A - Huang IC - Farzan M - Takahashi K - Stuart L - Stahl GL - Ezekowitz AB - Spear GT - Olinger GG - Schmidt EV - Michelow IC - - - 23342373 + LSECtin interacts with filovirus glycoproteins and the spike protein of SARS coronavirus. + Virology + 2005 + 16051304 PubMed - Endocytic pathways involved in filovirus entry: advances, implications and future directions. - Viruses - 2012 - Bhattacharyya S - Mulherkar N - Chandran K + LSECtin interacts with filovirus glycoproteins and the spike protein of SARS coronavirus. + Virology + 2005 + Gramberg T + Hofmann H + Moller P + Lalor PF + Marzi A + Geier M + Krumbiegel M + Winkler T + Kirchhoff F + Adams DH + Becker S + Munch J + Pohlmann S 26487564 @@ -2002,93 +1987,111 @@ This pathway was built using a text-mining approach to obtain interactions betwe Wang X Rao Z - - 17718913 + + 26468524 PubMed - New insights about host response to smallpox using microarray data. - BMC Syst Biol - 2007 - Esteves GH - Simoes AC - Souza E - Dias RA - Ospina R - Venancio TM + Ebolavirus Glycoprotein Directs Fusion through NPC1+ Endolysosomes. + J Virol + 2016 + Simmons JA + D'Souza RS + Ruas M + Galione A + Casanova JE + White JM - - 26516900 + + 11461707 PubMed - Requirements within the Ebola Viral Glycoprotein for Tetherin Antagonism. - Viruses - 2015 - Vande Burgt NH - Kaletsky RL - Bates P + Folate receptor-alpha is a cofactor for cellular entry by Marburg and Ebola viruses. + Cell + 2001 + Chan SY + Empig CJ + Welte FJ + Speck RF + Schmaljohn A + Kreisberg JF + Goldsmith MA - - 19694547 + + viral infectious disease + DOID:934 + Disease + + + 19153231 PubMed - Evasion of interferon responses by Ebola and Marburg viruses. - J Interferon Cytokine Res + Ebola virus protein VP35 impairs the function of interferon regulatory factor-activating kinases IKKepsilon and TBK-1. + J Virol + 2009 + 19153231 + PubMed + Ebola virus protein VP35 impairs the function of interferon regulatory factor-activating kinases IKKepsilon and TBK-1. + J Virol 2009 + Prins KC + Cardenas WB Basler CF - Amarasinghe GK - - 16140752 + + 17065211 PubMed - Rab9 GTPase is required for replication of human immunodeficiency virus type 1, filoviruses, and measles virus. + The VP35 protein of Ebola virus inhibits the antiviral effect mediated by double-stranded RNA-dependent protein kinase PKR. J Virol - 2005 - Murray JL - Mavrakis M - McDonald NJ - Yilla M - Sheng J - Bellini WJ - Zhao L - Le Doux JM - Shaw MW - Luo CC - Lippincott-Schwartz J - Sanchez A - Rubin DH - Hodge TW + 2007 + Feng Z + Cerveny M + Yan Z + He B - - 22031933 + + 23637409 PubMed - Cathepsin cleavage potentiates the Ebola virus glycoprotein to undergo a subsequent fusion-relevant conformational change. + Host IQGAP1 and Ebola virus VP40 interactions facilitate virus-like particle egress. J Virol - 2012 - Brecher M - Schornberg KL - Delos SE - Fusco ML - Saphire EO - White JM + 2013 + Lu J + Qu Y + Liu Y + Jambusaria R + Han Z + Ruthel G + Freedman BD + Harty RN - - 21866103 + + 15103332 PubMed - Ebola virus entry requires the cholesterol transporter Niemann-Pick C1. - Nature - 2011 - Carette JE - Raaben M - Wong AC - Herbert AS - Obernosterer G - Mulherkar N - Kuehne AI - Kranzusch PJ - Griffin AM - Ruthel G - Dal Cin P - Dye JM - Whelan SP - Chandran K - Brummelkamp TR + Ectodomain shedding of the glycoprotein GP of Ebola virus. + EMBO J + 2004 + 15103332 + PubMed + Ectodomain shedding of the glycoprotein GP of Ebola virus. + EMBO J + 2004 + Dolnik O + Volchkova V + Garten W + Carbonnelle C + Becker S + Kahnt J + Stroher U + Klenk HD + Volchkov V + + + 25741013 + PubMed + Ebola virus VP35 interaction with dynein LC8 regulates viral RNA synthesis. + J Virol + 2015 + Luthra P + Jordan DS + Leung DW + Amarasinghe GK + Basler CF 24473128 @@ -2103,145 +2106,32 @@ This pathway was built using a text-mining approach to obtain interactions betwe Qiu X Maury W - - 19625394 + + 16698996 PubMed - Rho GTPases modulate entry of Ebola virus and vesicular stomatitis virus pseudotyped vectors. + Ebola virus VP24 binds karyopherin alpha1 and blocks STAT1 nuclear accumulation. J Virol - 2009 - Quinn K - Brindley MA - Weller ML - Kaludov N - Kondratowicz A - Hunt CL - Sinn PL - McCray PB Jr - Stein CS - Davidson BL - Flick R - Mandell R - Staplin W - Maury W - Chiorini JA + 2006 + Reid SP + Leung LW + Hartman AL + Martinez O + Shaw ML + Carbonnelle C + Volchkov VE + Nichol ST + Basler CF - - 26468524 - PubMed - Ebolavirus Glycoprotein Directs Fusion through NPC1+ Endolysosomes. - J Virol - 2016 - Simmons JA - D'Souza RS - Ruas M - Galione A - Casanova JE - White JM - - - 26246577 - PubMed - Suppressor of Cytokine Signaling 3 Is an Inducible Host Factor That Regulates Virus Egress during Ebola Virus Infection. - J Virol - 2015 - Okumura A - Rasmussen AL - Halfmann P - Feldmann F - Yoshimura A - Feldmann H - Kawaoka Y - Harty RN - Katze MG - - - 18769720 - PubMed - Phosphoinositide-3 kinase-Akt pathway controls cellular entry of Ebola virus - - 2008 - Saeed MF - Kolokoltsov AA - Freiberg AN - Holbrook MR - Davey RA - - - 25741013 + + 26379663 PubMed - Ebola virus VP35 interaction with dynein LC8 regulates viral RNA synthesis. - J Virol + Targeting C-Type Lectin Receptors for Cancer Immunity. + Front Immunol 2015 - Luthra P - Jordan DS - Leung DW - Amarasinghe GK - Basler CF - - - 11017109 - PubMed - DC-SIGN-ICAM-2 interaction mediates dendritic cell trafficking. - Nat Immunol - 2000 - Geijtenbeek TB - Krooshoop DJ - Bleijs DA - van Vliet SJ - van Duijnhoven GC - Grabovsky V - Alon R - Figdor CG - van Kooyk Y - - - 23555248 - PubMed - TIM-family proteins promote infection of multiple enveloped viruses through virion-associated phosphatidylserine. - PLoS Pathog - 2013 - Jemielity S - Wang JJ - Chan YK - Ahmed AA - Li W - Monahan S - Bu X - Farzan M - Freeman GJ - Umetsu DT - Dekruyff RH - Choe H - - - 17339424 - PubMed - The DC-SIGN-related lectin LSECtin mediates antigen capture and pathogen binding by human myeloid cells. - Blood - 2007 - Dominguez-Soto A - Aragoneses-Fenoll L - Martin-Gayo E - Martinez-Prats L - Colmenares M - Naranjo-Gomez M - Borras FE - Munoz P - Zubiaur M - Toribio ML - Delgado R - Corbi AL - - - 17065211 - PubMed - The VP35 protein of Ebola virus inhibits the antiviral effect mediated by double-stranded RNA-dependent protein kinase PKR. - J Virol - 2007 - Feng Z - Cerveny M - Yan Z - He B + Yan H + Kamiya T + Suabjakyong P + Tsuji NM 26771495 @@ -2257,101 +2147,6 @@ This pathway was built using a text-mining approach to obtain interactions betwe Yan J Gao GF - - 14673115 - PubMed - In vivo oligomerization and raft localization of Ebola virus protein VP40 during vesicular budding. - Proc Natl Acad Sci U S A - 2003 - Panchal RG - Ruthel G - Kenny TA - Kallstrom GH - Lane D - Badie SS - Li L - Bavari S - Aman MJ - - - viral infectious disease - DOID:934 - Disease - - - 25396298 - PubMed - Immune evasion in ebolavirus infections. - Viral Immunol - 2015 - Audet J - Kobinger GP - - - 15103332 - PubMed - Ectodomain shedding of the glycoprotein GP of Ebola virus. - EMBO J - 2004 - 15103332 - PubMed - Ectodomain shedding of the glycoprotein GP of Ebola virus. - EMBO J - 2004 - Dolnik O - Volchkova V - Garten W - Carbonnelle C - Becker S - Kahnt J - Stroher U - Klenk HD - Volchkov V - - - 23637409 - PubMed - Host IQGAP1 and Ebola virus VP40 interactions facilitate virus-like particle egress. - J Virol - 2013 - Lu J - Qu Y - Liu Y - Jambusaria R - Han Z - Ruthel G - Freedman BD - Harty RN - - - 25493356 - PubMed - Ebola virus infection induces irregular dendritic cell gene expression. - Viral Immunol - 2015 - Melanson VR - Kalina WV - Williams P - - - 23870315 - PubMed - Mutual antagonism between the Ebola virus VP35 protein and the RIG-I activator PACT determines infection outcome. - Cell Host Microbe - 2013 - Luthra P - Ramanan P - Mire CE - Weisend C - Tsuda Y - Yen B - Liu G - Leung DW - Geisbert TW - Ebihara H - Amarasinghe GK - Basler CF - 17005688 PubMed @@ -2368,6 +2163,36 @@ This pathway was built using a text-mining approach to obtain interactions betwe Feldmann H Kawaoka Y + + 10975523 + PubMed + Developmental control of endocytosis in dendritic cells by Cdc42. + Cell + 2000 + 10975523 + PubMed + Developmental control of endocytosis in dendritic cells by Cdc42. + Cell + 2000 + Garrett WS + Chen LM + Kroschewski R + Ebersold M + Turley S + Trombetta S + Galan JE + Mellman I. + + + 21855102 + PubMed + Differential requirements for clathrin endocytic pathway components in cellular entry by Ebola and Marburg glycoprotein pseudovirions. + Virology + 2011 + Bhattacharyya S + Hope TJ + Young JA + 22383882 PubMed @@ -2383,75 +2208,47 @@ This pathway was built using a text-mining approach to obtain interactions betwe Woods VL Jr Saphire EO - - Ebola hemorrhagic fever - DOID:4325 - Disease - - - 25642836 + + 23573288 PubMed - Human lectins and their roles in viral infections. - Molecules - 2015 - Mason CP - Tarr AW - - - 16051304 - PubMed - LSECtin interacts with filovirus glycoproteins and the spike protein of SARS coronavirus. - Virology - 2005 - 16051304 - PubMed - LSECtin interacts with filovirus glycoproteins and the spike protein of SARS coronavirus. - Virology - 2005 - Gramberg T - Hofmann H - Moller P - Lalor PF - Marzi A - Geier M - Krumbiegel M - Winkler T - Kirchhoff F - Adams DH - Becker S - Munch J - Pohlmann S - - - 16698996 - PubMed - Ebola virus VP24 binds karyopherin alpha1 and blocks STAT1 nuclear accumulation. - J Virol - 2006 - Reid SP - Leung LW - Hartman AL - Martinez O - Shaw ML - Carbonnelle C - Volchkov VE - Nichol ST - Basler CF + Lectin-dependent enhancement of Ebola virus infection via soluble and transmembrane C-type lectin receptors. + PLoS One + 2013 + Brudner M + Karpel M + Lear C + Chen L + Yantosca LM + Scully C + Sarraju A + Sokolovska A + Zariffard MR + Eisen DP + Mungall BA + Kotton DN + Omari A + Huang IC + Farzan M + Takahashi K + Stuart L + Stahl GL + Ezekowitz AB + Spear GT + Olinger GG + Schmidt EV + Michelow IC - - 19153231 - PubMed - Ebola virus protein VP35 impairs the function of interferon regulatory factor-activating kinases IKKepsilon and TBK-1. - J Virol - 2009 - 19153231 + + 18769720 PubMed - Ebola virus protein VP35 impairs the function of interferon regulatory factor-activating kinases IKKepsilon and TBK-1. - J Virol - 2009 - Prins KC - Cardenas WB - Basler CF + Phosphoinositide-3 kinase-Akt pathway controls cellular entry of Ebola virus + + 2008 + Saeed MF + Kolokoltsov AA + Freiberg AN + Holbrook MR + Davey RA 25136083 @@ -2470,26 +2267,6 @@ This pathway was built using a text-mining approach to obtain interactions betwe Freed EO Liu SL - - 10975523 - PubMed - Developmental control of endocytosis in dendritic cells by Cdc42. - Cell - 2000 - 10975523 - PubMed - Developmental control of endocytosis in dendritic cells by Cdc42. - Cell - 2000 - Garrett WS - Chen LM - Kroschewski R - Ebersold M - Turley S - Trombetta S - Galan JE - Mellman I. - 24478428 PubMed @@ -2499,40 +2276,263 @@ This pathway was built using a text-mining approach to obtain interactions betwe Morizono K Chen IS - - 11461707 + + Ebola hemorrhagic fever + DOID:4325 + Disease + + + 19694547 PubMed - Folate receptor-alpha is a cofactor for cellular entry by Marburg and Ebola viruses. - Cell - 2001 - Chan SY - Empig CJ - Welte FJ - Speck RF - Schmaljohn A - Kreisberg JF - Goldsmith MA + Evasion of interferon responses by Ebola and Marburg viruses. + J Interferon Cytokine Res + 2009 + Basler CF + Amarasinghe GK - - 21855102 + + 25642836 PubMed - Differential requirements for clathrin endocytic pathway components in cellular entry by Ebola and Marburg glycoprotein pseudovirions. - Virology - 2011 + Human lectins and their roles in viral infections. + Molecules + 2015 + Mason CP + Tarr AW + + + 23555248 + PubMed + TIM-family proteins promote infection of multiple enveloped viruses through virion-associated phosphatidylserine. + PLoS Pathog + 2013 + Jemielity S + Wang JJ + Chan YK + Ahmed AA + Li W + Monahan S + Bu X + Farzan M + Freeman GJ + Umetsu DT + Dekruyff RH + Choe H + + + 22031933 + PubMed + Cathepsin cleavage potentiates the Ebola virus glycoprotein to undergo a subsequent fusion-relevant conformational change. + J Virol + 2012 + Brecher M + Schornberg KL + Delos SE + Fusco ML + Saphire EO + White JM + + + 23870315 + PubMed + Mutual antagonism between the Ebola virus VP35 protein and the RIG-I activator PACT determines infection outcome. + Cell Host Microbe + 2013 + Luthra P + Ramanan P + Mire CE + Weisend C + Tsuda Y + Yen B + Liu G + Leung DW + Geisbert TW + Ebihara H + Amarasinghe GK + Basler CF + + + 23342373 + PubMed + Endocytic pathways involved in filovirus entry: advances, implications and future directions. + Viruses + 2012 Bhattacharyya S - Hope TJ - Young JA + Mulherkar N + Chandran K - - 26379663 + + 19625394 PubMed - Targeting C-Type Lectin Receptors for Cancer Immunity. - Front Immunol + Rho GTPases modulate entry of Ebola virus and vesicular stomatitis virus pseudotyped vectors. + J Virol + 2009 + Quinn K + Brindley MA + Weller ML + Kaludov N + Kondratowicz A + Hunt CL + Sinn PL + McCray PB Jr + Stein CS + Davidson BL + Flick R + Mandell R + Staplin W + Maury W + Chiorini JA + + + 16140752 + PubMed + Rab9 GTPase is required for replication of human immunodeficiency virus type 1, filoviruses, and measles virus. + J Virol + 2005 + Murray JL + Mavrakis M + McDonald NJ + Yilla M + Sheng J + Bellini WJ + Zhao L + Le Doux JM + Shaw MW + Luo CC + Lippincott-Schwartz J + Sanchez A + Rubin DH + Hodge TW + + + 26246577 + PubMed + Suppressor of Cytokine Signaling 3 Is an Inducible Host Factor That Regulates Virus Egress during Ebola Virus Infection. + J Virol 2015 - Yan H - Kamiya T - Suabjakyong P - Tsuji NM + Okumura A + Rasmussen AL + Halfmann P + Feldmann F + Yoshimura A + Feldmann H + Kawaoka Y + Harty RN + Katze MG + + + 11017109 + PubMed + DC-SIGN-ICAM-2 interaction mediates dendritic cell trafficking. + Nat Immunol + 2000 + Geijtenbeek TB + Krooshoop DJ + Bleijs DA + van Vliet SJ + van Duijnhoven GC + Grabovsky V + Alon R + Figdor CG + van Kooyk Y + + + 17718913 + PubMed + New insights about host response to smallpox using microarray data. + BMC Syst Biol + 2007 + Esteves GH + Simoes AC + Souza E + Dias RA + Ospina R + Venancio TM + + + 17339424 + PubMed + The DC-SIGN-related lectin LSECtin mediates antigen capture and pathogen binding by human myeloid cells. + Blood + 2007 + Dominguez-Soto A + Aragoneses-Fenoll L + Martin-Gayo E + Martinez-Prats L + Colmenares M + Naranjo-Gomez M + Borras FE + Munoz P + Zubiaur M + Toribio ML + Delgado R + Corbi AL + + + 25396298 + PubMed + Immune evasion in ebolavirus infections. + Viral Immunol + 2015 + Audet J + Kobinger GP + + + 26516900 + PubMed + Requirements within the Ebola Viral Glycoprotein for Tetherin Antagonism. + Viruses + 2015 + Vande Burgt NH + Kaletsky RL + Bates P + + + 21866103 + PubMed + Ebola virus entry requires the cholesterol transporter Niemann-Pick C1. + Nature + 2011 + Carette JE + Raaben M + Wong AC + Herbert AS + Obernosterer G + Mulherkar N + Kuehne AI + Kranzusch PJ + Griffin AM + Ruthel G + Dal Cin P + Dye JM + Whelan SP + Chandran K + Brummelkamp TR + + + 25493356 + PubMed + Ebola virus infection induces irregular dendritic cell gene expression. + Viral Immunol + 2015 + Melanson VR + Kalina WV + Williams P + + + 14673115 + PubMed + In vivo oligomerization and raft localization of Ebola virus protein VP40 during vesicular budding. + Proc Natl Acad Sci U S A + 2003 + Panchal RG + Ruthel G + Kenny TA + Kallstrom GH + Lane D + Badie SS + Li L + Bavari S + Aman MJ 26861015 diff --git a/pathways/WP4217/WP4217.json b/pathways/WP4217/WP4217.json index 0146b0399..27070110c 100644 --- a/pathways/WP4217/WP4217.json +++ b/pathways/WP4217/WP4217.json @@ -17832,7 +17832,7 @@ "id": "publicationXrefa72", "source": "PLoS Pathog", "standardName": "The ebola virus interferon antagonist VP24 directly binds STAT1 and has a novel, pyramidal fold.", - "textContent": "21", + "textContent": "19", "type": [ "PublicationXref", "PubMed:22383882" @@ -17851,7 +17851,7 @@ "id": "publicationXrefb0a", "source": "Viruses", "standardName": "Requirements within the Ebola Viral Glycoprotein for Tetherin Antagonism.", - "textContent": "30", + "textContent": "35", "type": [ "PublicationXref", "PubMed:26516900" @@ -17873,7 +17873,7 @@ "id": "publicationXrefb10", "source": "BMC Syst Biol", "standardName": "New insights about host response to smallpox using microarray data.", - "textContent": "10", + "textContent": "11", "type": [ "PublicationXref", "PubMed:17718913" @@ -17942,7 +17942,7 @@ "id": "publicationXrefb97", "source": "J Virol", "standardName": "Ebola virus VP35 interaction with dynein LC8 regulates viral RNA synthesis.", - "textContent": "32", + "textContent": "30", "type": [ "PublicationXref", "PubMed:25741013" @@ -17970,7 +17970,7 @@ "id": "publicationXrefb9e", "source": "Blood", "standardName": "The DC-SIGN-related lectin LSECtin mediates antigen capture and pathogen binding by human myeloid cells.", - "textContent": "11", + "textContent": "12", "type": [ "PublicationXref", "PubMed:17339424" @@ -18000,7 +18000,7 @@ "id": "publicationXrefba2", "source": "J Virol", "standardName": "Rab9 GTPase is required for replication of human immunodeficiency virus type 1, filoviruses, and measles virus.", - "textContent": "6", + "textContent": "7", "type": [ "PublicationXref", "PubMed:16140752" @@ -18020,7 +18020,7 @@ "id": "publicationXrefbdd", "source": "J Virol", "standardName": "The VP35 protein of Ebola virus inhibits the antiviral effect mediated by double-stranded RNA-dependent protein kinase PKR.", - "textContent": "12", + "textContent": "10", "type": [ "PublicationXref", "PubMed:17065211" @@ -18051,7 +18051,7 @@ "id": "publicationXrefc4a", "source": "Nature", "standardName": "Ebola virus entry requires the cholesterol transporter Niemann-Pick C1.", - "textContent": "17", + "textContent": "18", "type": [ "PublicationXref", "PubMed:21866103" @@ -18070,7 +18070,7 @@ "id": "publicationXrefc79", "source": "Viruses", "standardName": "Endocytic pathways involved in filovirus entry: advances, implications and future directions.", - "textContent": "19", + "textContent": "21", "type": [ "PublicationXref", "PubMed:23342373" @@ -18135,7 +18135,7 @@ "id": "publicationXrefc9a", "source": "Front Immunol", "standardName": "Targeting C-Type Lectin Receptors for Cancer Immunity.", - "textContent": "36", + "textContent": "31", "type": [ "PublicationXref", "PubMed:26379663" @@ -18185,7 +18185,7 @@ "id": "publicationXrefcee", "source": "PLoS Pathog", "standardName": "TIM-family proteins promote infection of multiple enveloped viruses through virion-associated phosphatidylserine.", - "textContent": "23", + "textContent": "24", "type": [ "PublicationXref", "PubMed:23555248" @@ -18204,7 +18204,7 @@ "id": "publicationXrefd1c", "source": "Viral Immunol", "standardName": "Ebola virus infection induces irregular dendritic cell gene expression.", - "textContent": "34", + "textContent": "36", "type": [ "PublicationXref", "PubMed:25493356" @@ -18250,7 +18250,7 @@ "id": "publicationXrefd26", "source": "Nat Immunol", "standardName": "DC-SIGN-ICAM-2 interaction mediates dendritic cell trafficking.", - "textContent": "1", + "textContent": "2", "type": [ "PublicationXref", "PubMed:11017109" @@ -18274,7 +18274,7 @@ "id": "publicationXrefd51", "source": "Cell", "standardName": "Developmental control of endocytosis in dendritic cells by Cdc42.", - "textContent": "2", + "textContent": "1", "type": [ "PublicationXref", "PubMed:10975523" @@ -18303,7 +18303,7 @@ "id": "publicationXrefd90", "source": "Virology", "standardName": "LSECtin interacts with filovirus glycoproteins and the spike protein of SARS coronavirus.", - "textContent": "7", + "textContent": "6", "type": [ "PublicationXref", "PubMed:16051304" @@ -18322,7 +18322,7 @@ "id": "publicationXrefd9c", "source": "J Virol", "standardName": "Ebola virus protein VP35 impairs the function of interferon regulatory factor-activating kinases IKKepsilon and TBK-1.", - "textContent": "16", + "textContent": "14", "type": [ "PublicationXref", "PubMed:19153231" @@ -18373,7 +18373,7 @@ "id": "publicationXrefe99", "source": "J Virol", "standardName": "Tyro3 family-mediated cell entry of Ebola and Marburg viruses.", - "textContent": "8", + "textContent": "9", "type": [ "PublicationXref", "PubMed:17005688" @@ -18391,7 +18391,7 @@ "id": "publicationXrefead", "source": "Viral Immunol", "standardName": "Immune evasion in ebolavirus infections.", - "textContent": "33", + "textContent": "34", "type": [ "PublicationXref", "PubMed:25396298" @@ -18432,7 +18432,7 @@ "id": "publicationXreff33", "source": "Virology", "standardName": "Differential requirements for clathrin endocytic pathway components in cellular entry by Ebola and Marburg glycoprotein pseudovirions.", - "textContent": "18", + "textContent": "17", "type": [ "PublicationXref", "PubMed:21855102" @@ -18485,7 +18485,7 @@ "id": "publicationXreff69", "source": "J Virol", "standardName": "Ebola virus VP24 binds karyopherin alpha1 and blocks STAT1 nuclear accumulation.", - "textContent": "9", + "textContent": "8", "type": [ "PublicationXref", "PubMed:16698996" @@ -18503,7 +18503,7 @@ "id": "publicationXreff74", "source": "J Interferon Cytokine Res", "standardName": "Evasion of interferon responses by Ebola and Marburg viruses.", - "textContent": "14", + "textContent": "15", "type": [ "PublicationXref", "PubMed:19694547" @@ -18527,7 +18527,7 @@ "id": "publicationXreff7b", "source": "J Virol", "standardName": "Host IQGAP1 and Ebola virus VP40 interactions facilitate virus-like particle egress.", - "textContent": "24", + "textContent": "22", "type": [ "PublicationXref", "PubMed:23637409" @@ -18545,7 +18545,7 @@ "id": "publicationXreff8e", "source": "Molecules", "standardName": "Human lectins and their roles in viral infections.", - "textContent": "35", + "textContent": "32", "type": [ "PublicationXref", "PubMed:25642836" @@ -18576,7 +18576,7 @@ "id": "publicationXreff97", "source": "J Virol", "standardName": "Rho GTPases modulate entry of Ebola virus and vesicular stomatitis virus pseudotyped vectors.", - "textContent": "15", + "textContent": "16", "type": [ "PublicationXref", "PubMed:19625394" @@ -18619,7 +18619,7 @@ "id": "publicationXreffdb", "source": "J Virol", "standardName": "Suppressor of Cytokine Signaling 3 Is an Inducible Host Factor That Regulates Virus Egress during Ebola Virus Infection.", - "textContent": "31", + "textContent": "33", "type": [ "PublicationXref", "PubMed:26246577" @@ -18658,7 +18658,7 @@ "id": "publicationXreffe5", "source": "PLoS One", "standardName": "Lectin-dependent enhancement of Ebola virus infection via soluble and transmembrane C-type lectin receptors.", - "textContent": "22", + "textContent": "23", "type": [ "PublicationXref", "PubMed:23573288" diff --git a/pathways/WP4224/WP4224.gpml b/pathways/WP4224/WP4224.gpml index f7a8c393a..c386d8777 100644 --- a/pathways/WP4224/WP4224.gpml +++ b/pathways/WP4224/WP4224.gpml @@ -1916,13 +1916,13 @@ and aldehyde oxidase, named xanthinuria type II" Pathway Ontology - purine nucleoside phosphorylase deficiency pathway - PW:0001777 + purine metabolic pathway + PW:0000031 Pathway Ontology - mitochondrial DNA depletion syndrome 3 - DOID:0080121 + adenylosuccinase lyase deficiency + DOID:0050762 Disease @@ -1930,11 +1930,6 @@ and aldehyde oxidase, named xanthinuria type II" DOID:5810 Disease - - disease pathway - PW:0000013 - Pathway Ontology - 10.1016/B978-0-12-405546-9.00005-4 DOI @@ -1945,9 +1940,14 @@ and aldehyde oxidase, named xanthinuria type II" Lenardo, M. - adenylosuccinase lyase deficiency - DOID:0050762 - Disease + disease pathway + PW:0000013 + Pathway Ontology + + + purine nucleoside phosphorylase deficiency pathway + PW:0001777 + Pathway Ontology 9783642403361 @@ -1960,11 +1960,6 @@ and aldehyde oxidase, named xanthinuria type II" Gibson, K.M. Dionisi-Vici, C. - - purine metabolic pathway - PW:0000031 - Pathway Ontology - adenine phosphoribosyltransferase deficiency DOID:0060350 @@ -1978,11 +1973,6 @@ and aldehyde oxidase, named xanthinuria type II" 2013 R. Mendel - - adenosine monophosphate deaminase deficiency pathway - PW:0001779 - Pathway Ontology - 28939686 PubMed @@ -2000,6 +1990,16 @@ and aldehyde oxidase, named xanthinuria type II" PW:0001592 Pathway Ontology + + mitochondrial DNA depletion syndrome 3 + DOID:0080121 + Disease + + + adenosine monophosphate deaminase deficiency pathway + PW:0001779 + Pathway Ontology + Lesch-Nyhan syndrome DOID:1919 diff --git a/pathways/WP4224/WP4224.json b/pathways/WP4224/WP4224.json index ed3d336da..e2f223c24 100644 --- a/pathways/WP4224/WP4224.json +++ b/pathways/WP4224/WP4224.json @@ -19427,11 +19427,11 @@ "Pathway", "http://identifiers.org/pw/PW:0001776", "http://identifiers.org/pw/PW:0001879", - "http://identifiers.org/pw/PW:0001777", - "http://identifiers.org/pw/PW:0000013", "http://identifiers.org/pw/PW:0000031", - "http://identifiers.org/pw/PW:0001779", - "http://identifiers.org/pw/PW:0001592" + "http://identifiers.org/pw/PW:0000013", + "http://identifiers.org/pw/PW:0001777", + "http://identifiers.org/pw/PW:0001592", + "http://identifiers.org/pw/PW:0001779" ], "verticalAlign": "top", "width": 2357.1066152108338, diff --git a/pathways/WP4238/WP4238.gpml b/pathways/WP4238/WP4238.gpml index 7ad633051..80f19b4b8 100644 --- a/pathways/WP4238/WP4238.gpml +++ b/pathways/WP4238/WP4238.gpml @@ -1870,73 +1870,57 @@ Acknowledgements: This pathway is based upon work from COST Action POSITIVe, sup - - 21776473 - PubMed - Insights into the metabolism and microbial biotransformation of dietary flavan-3-ols and the bioactivity of their metabolites. - Food Funct - 2010 - Monagas M - Urpi-Sarda M - Sánchez-Patán F - Llorach R - Garrido I - Gómez-Cordovés C - Andres-Lacueva C - Bartolomé B - - - 24172307 + + 28125348 PubMed - Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols. - Am J Clin Nutr - 2013 + Anthocyanins and Flavanones Are More Bioavailable than Previously Perceived: A Review of Recent Evidence. + Annu Rev Food Sci Technol + 2017 + Kay CD + Pereira-Caro G + Ludwig IA Clifford MN - van der Hooft JJ Crozier A - - 20854839 - PubMed - Bioavailability of dietary flavonoids and phenolic compounds. - Mol Aspects Med - 2010 - Crozier A - Del Rio D - Clifford MN - - - 19636448 + + 19671472 PubMed - Dietary phenolics: chemistry, bioavailability and effects on health. - Nat Prod Rep + Targeted metabolic profiling of phenolics in urine and plasma after regular consumption of cocoa by liquid chromatography-tandem mass spectrometry. + J Chromatogr A 2009 - Crozier A - Jaganath IB - Clifford MN + Urpi-Sarda M + Monagas M + Khan N + Llorach R + Lamuela-Raventós RM + Jáuregui O + Estruch R + Izquierdo-Pulido M + Andrés-Lacueva C - - 25182418 + + 20931601 PubMed - Bioavailability, bioactivity and impact on health of dietary flavonoids and related compounds: an update. - Arch Toxicol - 2014 - Rodriguez-Mateos A - Vauzour D - Krueger CG - Shanmuganayagam D - Reed J - Calani L - Mena P - Del Rio D - Crozier A + Metabolism of green tea catechins by the human small intestine. + Biotechnol J + 2010 + Schantz M + Erk T + Richling E - - 28595385 + + 20726519 PubMed - Identification and expression analysis of genes involved in anthocyanin and proanthocyanidin biosynthesis in the fruit of blackberry - - 2012 + In vitro bioconversion of polyphenols from black tea and red wine/grape juice by human intestinal microbiota displays strong interindividual variability. + J Agric Food Chem + 2010 + Gross G + Jacobs DM + Peters S + Possemiers S + van Duynhoven J + Vaughan EE + van de Wiele T 27495388 @@ -1953,40 +1937,53 @@ Acknowledgements: This pathway is based upon work from COST Action POSITIVe, sup van der Hooft JJJ Crozier A - - 21457417 + + 10.1021/ac3017339 + DOI + Trypsin-catalyzed activation of aspartase. + Biochem Biophys Res Commun + 1975 + 22827565 PubMed - Isolation of catechin-converting human intestinal bacteria. - J Appl Microbiol - 2011 - Kutschera M - Engst W - Blaut M - Braune A + Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake. + Anal Chem + 2012 + van der Hooft JJ + de Vos RC + Mihaleva V + Bino RJ + Ridder L + de Roo N + Jacobs DM + van Duynhoven JP + Vervoort J - - 9929521 + + 24172307 PubMed - Identification of (-)-epicatechin metabolites and their metabolic fate in the rat. - Drug Metab Dispos - 1999 - Okushio K - Suzuki M - Matsumoto N - Nanjo F - Hara Y + Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols. + Am J Clin Nutr + 2013 + Clifford MN + van der Hooft JJ + Crozier A - - 28125348 + + 28595385 PubMed - Anthocyanins and Flavanones Are More Bioavailable than Previously Perceived: A Review of Recent Evidence. - Annu Rev Food Sci Technol - 2017 - Kay CD - Pereira-Caro G - Ludwig IA - Clifford MN + Identification and expression analysis of genes involved in anthocyanin and proanthocyanidin biosynthesis in the fruit of blackberry + + 2012 + + + 19636448 + PubMed + Dietary phenolics: chemistry, bioavailability and effects on health. + Nat Prod Rep + 2009 Crozier A + Jaganath IB + Clifford MN 28595385 @@ -2002,39 +1999,26 @@ Acknowledgements: This pathway is based upon work from COST Action POSITIVe, sup Hara Y Crozier A - - 20041649 - PubMed - Green tea flavan-3-ols: colonic degradation and urinary excretion of catabolites by humans. - J Agric Food Chem - 2010 - Roowi S - Stalmach A - Mullen W - Lean ME - Edwards CA - Crozier A - - - 22254058 + + 1967147 PubMed - Bioavailability of coffee chlorogenic acids and green tea flavan-3-ols. - Nutrients - 2010 - Del Rio D - Stalmach A - Calani L - Crozier A - - - 20931601 + The current distribution of CD4+ T-lymphocyte counts among adultsin the United States with human immunodeficiency virus infections: estimates based on the experience of the U.S. Army. U.S. Army Retrovirus Research Group. + J Acquir Immune Defic Syndr + 1990 + 19671472 PubMed - Metabolism of green tea catechins by the human small intestine. - Biotechnol J - 2010 - Schantz M - Erk T - Richling E + Targeted metabolic profiling of phenolics in urine and plasma after regular consumption of cocoa by liquid chromatography-tandem mass spectrometry. + J Chromatogr A + 2009 + Urpi-Sarda M + Monagas M + Khan N + Llorach R + Lamuela-Raventós RM + Jáuregui O + Estruch R + Izquierdo-Pulido M + Andrés-Lacueva C 22240152 @@ -2048,50 +2032,53 @@ Acknowledgements: This pathway is based upon work from COST Action POSITIVe, sup Keen CL Schroeter H - - 20955651 - PubMed - Berry flavonoids and phenolics: bioavailability and evidence of protective effects. - Br J Nutr - 2010 - Del Rio D - Borges G - Crozier A - - - 10.1021/ac3017339 - DOI - Trypsin-catalyzed activation of aspartase. - Biochem Biophys Res Commun - 1975 - 22827565 + + 22664313 PubMed - Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake. - Anal Chem + Elucidation of (-)-epicatechin metabolites after ingestion of chocolate by healthy humans. + Free Radic Biol Med 2012 - van der Hooft JJ - de Vos RC - Mihaleva V - Bino RJ - Ridder L - de Roo N - Jacobs DM - van Duynhoven JP - Vervoort J + Actis-Goretta L + Lévèques A + Giuffrida F + Romanov-Michailidis F + Viton F + Barron D + Duenas-Paton M + Gonzalez-Manzano S + Santos-Buelga C + Williamson G + Dionisi F - - 20726519 + + classic metabolic pathway + PW:0000002 + Pathway Ontology + + + 20041649 PubMed - In vitro bioconversion of polyphenols from black tea and red wine/grape juice by human intestinal microbiota displays strong interindividual variability. + Green tea flavan-3-ols: colonic degradation and urinary excretion of catabolites by humans. J Agric Food Chem 2010 - Gross G - Jacobs DM - Peters S - Possemiers S - van Duynhoven J - Vaughan EE - van de Wiele T + Roowi S + Stalmach A + Mullen W + Lean ME + Edwards CA + Crozier A + + + 9929521 + PubMed + Identification of (-)-epicatechin metabolites and their metabolic fate in the rat. + Drug Metab Dispos + 1999 + Okushio K + Suzuki M + Matsumoto N + Nanjo F + Hara Y 24602005 @@ -2107,23 +2094,57 @@ Acknowledgements: This pathway is based upon work from COST Action POSITIVe, sup Cassidy A Kay CD - - 22664313 + + 21776473 PubMed - Elucidation of (-)-epicatechin metabolites after ingestion of chocolate by healthy humans. - Free Radic Biol Med - 2012 - Actis-Goretta L - Lévèques A - Giuffrida F - Romanov-Michailidis F - Viton F - Barron D - Duenas-Paton M - Gonzalez-Manzano S - Santos-Buelga C - Williamson G - Dionisi F + Insights into the metabolism and microbial biotransformation of dietary flavan-3-ols and the bioactivity of their metabolites. + Food Funct + 2010 + Monagas M + Urpi-Sarda M + Sánchez-Patán F + Llorach R + Garrido I + Gómez-Cordovés C + Andres-Lacueva C + Bartolomé B + + + 22254058 + PubMed + Bioavailability of coffee chlorogenic acids and green tea flavan-3-ols. + Nutrients + 2010 + Del Rio D + Stalmach A + Calani L + Crozier A + + + 25182418 + PubMed + Bioavailability, bioactivity and impact on health of dietary flavonoids and related compounds: an update. + Arch Toxicol + 2014 + Rodriguez-Mateos A + Vauzour D + Krueger CG + Shanmuganayagam D + Reed J + Calani L + Mena P + Del Rio D + Crozier A + + + 20854839 + PubMed + Bioavailability of dietary flavonoids and phenolic compounds. + Mol Aspects Med + 2010 + Crozier A + Del Rio D + Clifford MN 16115350 @@ -2139,47 +2160,26 @@ Acknowledgements: This pathway is based upon work from COST Action POSITIVe, sup Crozier A Teissedre PL - - classic metabolic pathway - PW:0000002 - Pathway Ontology - - - 1967147 - PubMed - The current distribution of CD4+ T-lymphocyte counts among adultsin the United States with human immunodeficiency virus infections: estimates based on the experience of the U.S. Army. U.S. Army Retrovirus Research Group. - J Acquir Immune Defic Syndr - 1990 - 19671472 + + 20955651 PubMed - Targeted metabolic profiling of phenolics in urine and plasma after regular consumption of cocoa by liquid chromatography-tandem mass spectrometry. - J Chromatogr A - 2009 - Urpi-Sarda M - Monagas M - Khan N - Llorach R - Lamuela-Raventós RM - Jáuregui O - Estruch R - Izquierdo-Pulido M - Andrés-Lacueva C + Berry flavonoids and phenolics: bioavailability and evidence of protective effects. + Br J Nutr + 2010 + Del Rio D + Borges G + Crozier A - - 19671472 + + 21457417 PubMed - Targeted metabolic profiling of phenolics in urine and plasma after regular consumption of cocoa by liquid chromatography-tandem mass spectrometry. - J Chromatogr A - 2009 - Urpi-Sarda M - Monagas M - Khan N - Llorach R - Lamuela-Raventós RM - Jáuregui O - Estruch R - Izquierdo-Pulido M - Andrés-Lacueva C + Isolation of catechin-converting human intestinal bacteria. + J Appl Microbiol + 2011 + Kutschera M + Engst W + Blaut M + Braune A diff --git a/pathways/WP4238/WP4238.json b/pathways/WP4238/WP4238.json index 2ce20c678..9b215cda2 100644 --- a/pathways/WP4238/WP4238.json +++ b/pathways/WP4238/WP4238.json @@ -14334,7 +14334,7 @@ "id": "publicationXrefa13", "source": "J Agric Food Chem", "standardName": "In vitro bioconversion of polyphenols from black tea and red wine/grape juice by human intestinal microbiota displays strong interindividual variability.", - "textContent": "12", + "textContent": "7", "type": [ "PublicationXref", "PubMed:20726519" @@ -14358,7 +14358,7 @@ "id": "publicationXrefa6c", "source": "Food Funct", "standardName": "Insights into the metabolism and microbial biotransformation of dietary flavan-3-ols and the bioactivity of their metabolites.", - "textContent": "6", + "textContent": "9", "type": [ "PublicationXref", "PubMed:21776473" @@ -14383,7 +14383,7 @@ "id": "publicationXrefac8", "source": "J Chromatogr A", "standardName": "Targeted metabolic profiling of phenolics in urine and plasma after regular consumption of cocoa by liquid chromatography-tandem mass spectrometry.", - "textContent": "5", + "textContent": "3", "type": [ "PublicationXref", "PubMed:19671472" @@ -14406,7 +14406,7 @@ "id": "publicationXrefae3", "source": "Br J Pharmacol", "standardName": "The pharmacokinetics of anthocyanins and their metabolites in humans.", - "textContent": "20", + "textContent": "19", "type": [ "PublicationXref", "PubMed:24602005" @@ -14431,7 +14431,7 @@ "id": "publicationXrefbbc", "source": "Arch Toxicol", "standardName": "Bioavailability, bioactivity and impact on health of dietary flavonoids and related compounds: an update.", - "textContent": "19", + "textContent": "20", "type": [ "PublicationXref", "PubMed:25182418" @@ -14450,7 +14450,7 @@ "id": "publicationXrefc03", "source": "Mol Aspects Med", "standardName": "Bioavailability of dietary flavonoids and phenolic compounds.", - "textContent": "7", + "textContent": "11", "type": [ "PublicationXref", "PubMed:20854839" @@ -14463,7 +14463,7 @@ "gpmlElementName": "PublicationXref", "id": "publicationXrefc1c", "standardName": "Identification and expression analysis of genes involved in anthocyanin and proanthocyanidin biosynthesis in the fruit of blackberry", - "textContent": "14", + "textContent": "15", "type": [ "PublicationXref", "PubMed:28595385" @@ -14555,7 +14555,7 @@ "id": "publicationXrefd6b", "source": "Free Radic Biol Med", "standardName": "Structurally related (-)-epicatechin metabolites in humans: assessment using de novo chemically synthesized authentic standards.", - "textContent": "15", + "textContent": "16", "type": [ "PublicationXref", "PubMed:22240152" @@ -14593,7 +14593,7 @@ "id": "publicationXrefd9f", "source": "Br J Nutr", "standardName": "Berry flavonoids and phenolics: bioavailability and evidence of protective effects.", - "textContent": "11", + "textContent": "12", "type": [ "PublicationXref", "PubMed:20955651" @@ -14618,7 +14618,7 @@ "id": "publicationXrefdcf", "source": "Anal Chem", "standardName": "Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake.", - "textContent": "16", + "textContent": "14", "type": [ "PublicationXref", "PubMed:22827565" @@ -14661,7 +14661,7 @@ "id": "publicationXrefe47", "source": "Nutrients", "standardName": "Bioavailability of coffee chlorogenic acids and green tea flavan-3-ols.", - "textContent": "9", + "textContent": "10", "type": [ "PublicationXref", "PubMed:22254058" @@ -14768,7 +14768,7 @@ "id": "publicationXreff3e", "source": "J Chromatogr A", "standardName": "Targeted metabolic profiling of phenolics in urine and plasma after regular consumption of cocoa by liquid chromatography-tandem mass spectrometry.", - "textContent": "4", + "textContent": "5", "type": [ "PublicationXref", "PubMed:19671472" @@ -14787,7 +14787,7 @@ "id": "publicationXreff69", "source": "Nat Prod Rep", "standardName": "Dietary phenolics: chemistry, bioavailability and effects on health.", - "textContent": "3", + "textContent": "4", "type": [ "PublicationXref", "PubMed:19636448" @@ -14806,7 +14806,7 @@ "id": "publicationXreff8f", "source": "Biotechnol J", "standardName": "Metabolism of green tea catechins by the human small intestine.", - "textContent": "10", + "textContent": "6", "type": [ "PublicationXref", "PubMed:20931601" diff --git a/pathways/WP4298/WP4298.gpml b/pathways/WP4298/WP4298.gpml index 00c2a0f6b..b992054f9 100644 --- a/pathways/WP4298/WP4298.gpml +++ b/pathways/WP4298/WP4298.gpml @@ -2455,39 +2455,40 @@ Lancet 1986;1:1120-1123. - - 28912259 + + 16170679 PubMed - NOD2 (Nucleotide-Binding Oligomerization Domain 2) Is a Major Pathogenic Mediator of Coxsackievirus B3-Induced Myocarditis. - Circ Heart Fail - 2017 - Tschöpe C - Müller I - Xia Y - Savvatis K - Pappritz K - Pinkert S - Lassner D - Heimesaat MM - Spillmann F - Miteva K - Bereswill S - Schultheiss HP - Fechner H - Pieske B - Kühl U - Van Linthout S + HIV-associated cardiomyopathy etiopathogenesis and clinical aspects. + Herz + 2005 + Barbaro G - - 9108473 + + 12089062 PubMed - DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis. - Cell - 1997 - Liu X - Zou H - Slaughter C - Wang X + Nip21 gene expression reduces coxsackievirus B3 replication by promoting apoptotic cell death via a mitochondria-dependent pathway. + Circ Res + 2002 + Zhang HM + Yanagawa B + Cheung P + Luo H + Yuan J + Chau D + Wang A + Bohunek L + Wilson JE + McManus BM + Yang D + + + 9971843 + PubMed + Coxsackievirus and adenovirus receptor cytoplasmic and transmembrane domains are not essential for coxsackievirus and adenovirus infection. + J. Virol + 1999 + Wang, X. + Bergelson, J.M. 9616213 @@ -2502,46 +2503,10 @@ Lancet 1986;1:1120-1123. Leiden JM - CD4-positive, alpha-beta T cell - CL:0000624 + professional antigen presenting cell + CL:0000145 Cell Type - - 15371627 - PubMed - HIV-1 induces cardiomyopathyby cardiomyocyte invasion and gp120, Tat, and cytokine apoptotic signaling. - Cardiovasc Toxicol - 2004 - Fiala M - Popik W - Qiao JH - Lossinsky AS - Alce T - Tran K - Yang W - Roos KP - Arthos J - - - 9770555 - PubMed - Incidence of dilated cardiomyopathy and detection of HIV in myocardial cells of HIV-positive patients. Gruppo Italiano per lo Studio Cardiologico dei Pazienti Affetti da AIDS. - N Engl J Med - 1998 - Barbaro G - Di Lorenzo G - Grisorio B - Barbarini G - - - 15818401 - PubMed - DAP5 and IRES-mediated translation during programmed cell death. - Cell Death Differ - 2005 - Marash L - Kimchi A - 11762996 PubMed @@ -2551,36 +2516,45 @@ Lancet 1986;1:1120-1123. Barbaro G Lipshultz SE - - 17195095 + + viral infectious disease + DOID:934 + Disease + + + 22160858 PubMed - Coxsackievirus B3 proteases 2A and 3C induce apoptotic cell death through mitochondrial injury and cleavage of eIF4GI but not DAP5/p97/NAT1. - Apoptosis - 2007 - Chau DH - Yuan J - Zhang H - Cheung P - Lim T - Liu Z - Sall A - Yang D + Endonuclease G interacts with histone H2B and DNA topoisomerase II alpha during apoptosis. + Mol Cell Biochem + 2012 + Vařecha M + Potěšilová M + Matula P + Kozubek M - - 17195095 + + 15177891 PubMed - 2007 + 2004 PubMed - Coxsackievirus B3 proteases 2A and 3c induce apoptotix cell death through mitochondrial injury and cleavage of eIF4GI but not DAP5/p97/NAT1. - - 2007 - Chau, D. - Yuan, J. - Zhang, H. - et al. + Individual expression of poliovirus 2Apro and 3Cpro induces activation of caspase-3 and PARP cleavage in HeLa cells. + Virus Res 104:39-49 + 2004 + Calandria, C. + Irurzun, A. + Barco, A. + Carrasco, L. + + + 18357777 + PubMed + CVB infection and mechanisms of viral cardiomyopathy. + Curr Top Microbiol Immunol + 2008 + Knowlton KU 9321539 @@ -2590,52 +2564,106 @@ Lancet 1986;1:1120-1123. 1997 Leiden JM - - 15177891 + + 18039131 + PubMed + Molecular Biology and Pathogenesis of Viral Myocarditis; Annual Review of Pathology + Mechanisms of Disease + 2008 + Esfandiarei, M. + McManus, B.M. + + + 8591043 + PubMed + The structure of coxsackievirus B3 at 3.5 A resolution. + Structure + 1995 + Muckelbauer JK + Kremer M + Minor I + Diana G + Dutko FJ + Groarke J + Pevear DC + Rossmann MG + + + 17195095 PubMed - 2004 + 2007 PubMed - Individual expression of poliovirus 2Apro and 3Cpro induces activation of caspase-3 and PARP cleavage in HeLa cells. - Virus Res 104:39-49 - 2004 - Calandria, C. - Irurzun, A. - Barco, A. - Carrasco, L. + Coxsackievirus B3 proteases 2A and 3c induce apoptotix cell death through mitochondrial injury and cleavage of eIF4GI but not DAP5/p97/NAT1. + + 2007 + Chau, D. + Yuan, J. + Zhang, H. + et al. - - cardiac muscle cell - CL:0000746 - Cell Type - - - cardiomyopathy pathway - PW:0000022 - Pathway Ontology - - - 9727492 + + 12379743 PubMed - Cleavage of BID by caspase 8 mediates the mitochondrial damage in the Fas pathway of apoptosis. - Cell + Cardiomyocytes undergo apoptosis in human immunodeficiency virus cardiomyopathy through mitochondrion- and death receptor-controlled pathways. + Proc Natl Acad Sci U S A + 2002 + Twu C + Liu NQ + Popik W + Bukrinsky M + Sayre J + Roberts J + Rania S + Bramhandam V + Roos KP + MacLellan WR + Fiala M + + + 9770555 + PubMed + Incidence of dilated cardiomyopathy and detection of HIV in myocardial cells of HIV-positive patients. 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Lüscher TF Eriksson U - - myocarditis pathway - PW:0001037 - Pathway Ontology - - - 12089062 + + 9108473 PubMed - Nip21 gene expression reduces coxsackievirus B3 replication by promoting apoptotic cell death via a mitochondria-dependent pathway. - Circ Res - 2002 - Zhang HM - Yanagawa B - Cheung P - Luo H - Yuan J - Chau D - Wang A - Bohunek L - Wilson JE - McManus BM - Yang D + DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis. + Cell + 1997 + Liu X + Zou H + Slaughter C + Wang X - - 9971843 + + 17116881 PubMed - Coxsackievirus and adenovirus receptor cytoplasmic and transmembrane domains are not essential for coxsackievirus and adenovirus infection. - J. 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J Virol - 1999 + 1997 Huber M - Watson KA Selinka HC - Carthy CM - Klingel K - McManus BM Kandolf R - - 10.1016/j.yjmcc.2012.01.010 - DOI - Myocardial edema: A translational view - ScienceDirect - 2011 - Garcia-Dorado, D. - Andres-Villarreal, M. - Ruiz-Meana, M. - Inserte, J. - Barba, I. - - CD8-positive, alpha-beta T cell - CL:0000625 - Cell Type + myocarditis + DOID:820 + Disease - - 8591043 - PubMed - The structure of coxsackievirus B3 at 3.5 A resolution. - Structure - 1995 - Muckelbauer JK - Kremer M - Minor I - Diana G - Dutko FJ - Groarke J - Pevear DC - Rossmann MG - - - 11573093 + + myocarditis pathway + PW:0001037 + Pathway Ontology + + + 11779719 PubMed - Interaction of coxsackievirus B3 with the full length coxsackievirus-adenovirus receptor. - Nat Struct Biol - 2001 - He Y - Chipman PR - Howitt J - Bator CM - Whitt MA - Baker TS - Kuhn RJ - Anderson CW - Freimuth P - Rossmann MG + Bax and BH3-domain-only proteins in p53-mediated apoptosis. + Front Biosci + 2002 + Wu X + Deng Y - - 17116881 + + 15371627 PubMed - Apoptosis-inducing factor mediates poly(ADP-ribose) (PAR) polymer-induced cell death. - Proc Natl Acad Sci U S A - 2006 - Yu SW - Andrabi SA - Wang H - Kim NS - Poirier GG - Dawson TM - Dawson VL + HIV-1 induces cardiomyopathyby cardiomyocyte invasion and gp120, Tat, and cytokine apoptotic signaling. + Cardiovasc Toxicol + 2004 + Fiala M + Popik W + Qiao JH + Lossinsky AS + Alce T + Tran K + Yang W + Roos KP + Arthos J diff --git a/pathways/WP4298/WP4298.json b/pathways/WP4298/WP4298.json index a2802f5ef..063c6bcce 100644 --- a/pathways/WP4298/WP4298.json +++ b/pathways/WP4298/WP4298.json @@ -22699,7 +22699,7 @@ "id": "publicationXrefa29", "source": "Virus Res 104:39-49", "standardName": "Individual expression of poliovirus 2Apro and 3Cpro induces activation of caspase-3 and PARP cleavage in HeLa cells.", - "textContent": "26", + "textContent": "25", "type": [ "PublicationXref" ], @@ -22714,7 +22714,7 @@ "id": "publicationXrefa34", "source": "Herz", "standardName": "HIV-associated cardiomyopathy etiopathogenesis and clinical aspects.", - "textContent": "30", + "textContent": "28", "type": [ "PublicationXref", "PubMed:16170679" @@ -22733,7 +22733,7 @@ "id": "publicationXrefa5b", "source": "J Virol", "standardName": "Tyrosine phosphorylation events during coxsackievirus B3 replication.", - "textContent": "8", + "textContent": "9", "type": [ "PublicationXref", "PubMed:8985388" @@ -22755,7 +22755,7 @@ "id": "publicationXrefa9a", "source": "AIDS Res Hum Retroviruses", "standardName": "Essential role of HIV type 1-infected and cyclooxygenase 2-activated macrophages and T cells in HIV type 1 myocarditis.", - "textContent": "20", + "textContent": "21", "type": [ "PublicationXref", "PubMed:11679155" @@ -22772,7 +22772,7 @@ "id": "publicationXrefaa1", "source": "N Engl J Med", "standardName": "The genetics of dilated cardiomyopathy--emerging clues to the puzzle.", - "textContent": "7", + "textContent": "6", "type": [ "PublicationXref", "PubMed:9321539" @@ -22860,7 +22860,7 @@ "id": "publicationXrefb1e", "source": "Science", "standardName": "Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR.", - "textContent": "14", + "textContent": "15", "type": [ "PublicationXref", "PubMed:10567268" @@ -22996,7 +22996,7 @@ "id": "publicationXrefc23", "source": "J Virol", "standardName": "Cleavage of RasGAP and phosphorylation of mitogen-activated protein kinase in the course of coxsackievirus B3 replication.", - "textContent": "15", + "textContent": "14", "type": [ "PublicationXref", "PubMed:10196249" @@ -23060,7 +23060,7 @@ "id": "publicationXrefcb7", "source": "Nat Immunol", "standardName": "Activation of innate immune antiviral responses by Nod2.", - "textContent": "39", + "textContent": "38", "type": [ "PublicationXref", "PubMed:19701189" @@ -23118,7 +23118,7 @@ "gpmlElementName": "PublicationXref", "id": "publicationXrefd17", "standardName": "Coxsackievirus B3 proteases 2A and 3c induce apoptotix cell death through mitochondrial injury and cleavage of eIF4GI but not DAP5/p97/NAT1.", - "textContent": "33", + "textContent": "32", "type": [ "PublicationXref" ], @@ -23136,7 +23136,7 @@ "id": "publicationXrefd5e", "source": "Cell", "standardName": "DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis.", - "textContent": "6", + "textContent": "7", "type": [ "PublicationXref", "PubMed:9108473" @@ -23155,7 +23155,7 @@ "id": "publicationXrefd8f", "source": "Trends Cardiovasc Med", "standardName": "Mechanisms of cardiac fibrosis in inflammatory heart disease.", - "textContent": "38", + "textContent": "39", "type": [ "PublicationXref", "PubMed:20447565" @@ -23232,7 +23232,7 @@ "id": "publicationXrefdf3", "source": "Apoptosis", "standardName": "Coxsackievirus B3 proteases 2A and 3C induce apoptotic cell death through mitochondrial injury and cleavage of eIF4GI but not DAP5/p97/NAT1.", - "textContent": "32", + "textContent": "33", "type": [ "PublicationXref", "PubMed:17195095" @@ -23342,7 +23342,7 @@ "id": "publicationXrefeb4", "source": "Science", "standardName": "Isolation of a common receptor for Coxsackie B viruses and adenoviruses 2 and 5.", - "textContent": "9", + "textContent": "8", "type": [ "PublicationXref", "PubMed:9036860" @@ -23426,7 +23426,7 @@ "id": "publicationXreff4c", "source": "Cardiovasc Toxicol", "standardName": "HIV-1 induces cardiomyopathyby cardiomyocyte invasion and gp120, Tat, and cytokine apoptotic signaling.", - "textContent": "25", + "textContent": "27", "type": [ "PublicationXref", "PubMed:15371627" @@ -23445,7 +23445,7 @@ "id": "publicationXreff4d", "source": "Autoimmun Rev", "standardName": "Autoimmune myocarditis: cellular mediators of cardiac dysfunction.", - "textContent": "27", + "textContent": "26", "type": [ "PublicationXref", "PubMed:15546794" @@ -23463,7 +23463,7 @@ "id": "publicationXreff61", "source": "Annu Rev Pathol", "standardName": "Molecular biology and pathogenesis of viral myocarditis.", - "textContent": "34", + "textContent": "36", "type": [ "PublicationXref", "PubMed:18039131" @@ -23512,7 +23512,7 @@ "id": "publicationXreff91", "source": "Nat Struct Biol", "standardName": "Interaction of coxsackievirus B3 with the full length coxsackievirus-adenovirus receptor.", - "textContent": "21", + "textContent": "20", "type": [ "PublicationXref", "PubMed:11573093" @@ -23529,7 +23529,7 @@ "id": "publicationXreff97", "source": "Curr Top Microbiol Immunol", "standardName": "CVB infection and mechanisms of viral cardiomyopathy.", - "textContent": "36", + "textContent": "34", "type": [ "PublicationXref", "PubMed:18357777" @@ -23571,7 +23571,7 @@ "id": "publicationXreffd5", "source": "Cell Death Differ", "standardName": "DAP5 and IRES-mediated translation during programmed cell death.", - "textContent": "28", + "textContent": "30", "type": [ "PublicationXref", "PubMed:15818401" @@ -24067,8 +24067,8 @@ "type": [ "Pathway", "http://identifiers.org/pw/PW:0000022", - "http://identifiers.org/pw/PW:0001037", - "http://identifiers.org/pw/PW:0000013" + "http://identifiers.org/pw/PW:0000013", + "http://identifiers.org/pw/PW:0001037" ], "verticalAlign": "top", "width": 2892.5171940824193, diff --git a/pathways/WP4312/WP4312.gpml b/pathways/WP4312/WP4312.gpml index 482aa7e61..bed22d268 100644 --- a/pathways/WP4312/WP4312.gpml +++ b/pathways/WP4312/WP4312.gpml @@ -613,6 +613,27 @@ + + 19623215 + PubMed + Atypical Rett syndrome with selective FOXG1 deletion detected by comparative genomic hybridization: case report and review of literature. + Eur J Hum Genet + 2009 + Jacob FD + Ramaswamy V + Andersen J + Bolduc FV + + + 11238932 + PubMed + The winged-helix protein brain factor 1 interacts with groucho and hes proteins to repress transcription. + Mol Cell Biol + 2001 + Yao J + Lai E + Stifani S + 10611234 PubMed @@ -623,32 +644,6 @@ Wood MA Cole MD - 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Eur J Hum Genet - 2009 - Jacob FD - Ramaswamy V - Andersen J - Bolduc FV + Turinsky AL + Li Z + Wang PI + Boutz DR + Fong V + Phanse S + Babu M + Craig SA + Hu P + Wan C + Vlasblom J + Dar VU + Bezginov A + Clark GW + Wu GC + Wodak SJ + Tillier ER + Paccanaro A + Marcotte EM + Emili A 24920159 @@ -714,65 +700,52 @@ Yu F Cristea IM - - 15640247 + + 19262167 PubMed - CECR2, a protein involved in neurulation, forms a novel chromatin remodeling complex with SNF2L. - Hum Mol Genet - 2005 - Banting GS - Barak O - Ames TM - Burnham AC - Kardel MD - Cooch NS - Davidson CE - Godbout R - McDermid HE - Shiekhattar R + Huntingtin associated protein 1 and its functions. + Cell Adh Migr + 2009 + Wu LL + Zhou XF - - 11238932 + + disease pathway + PW:0000013 + Pathway Ontology + + + 15752761 PubMed - The winged-helix protein brain factor 1 interacts with groucho and hes proteins to repress transcription. - Mol Cell Biol - 2001 - Yao J - Lai E - Stifani S + PARG1, a protein-tyrosine phosphatase-associated RhoGAP, as a putative Rap2 effector. + Biochem Biophys Res Commun + 2005 + Myagmar BE + Umikawa M + Asato T + Taira K + Oshiro M + Hino A + Takei K + Uezato H + Kariya K - - 24662006 + + 24164323 PubMed - Dysregulation of the IGF-I/PI3K/AKT/mTOR signaling pathway in autism spectrum disorders. - Int J Dev Neurosci + Identification of two novel Shank3 transcripts in the developing mouse neocortex. + J Neurochem 2014 - Chen J - Alberts I - Li X - - - 27507650 - PubMed - Long-term potentiation modulates synaptic phosphorylation networks and reshapes the structure of the postsynaptic interactome. - Sci Signal - 2016 - Li J - Wilkinson B - Clementel VA - Hou J - O'Dell TJ - Coba MP - - - 10.1093/jcag/gwy009.249 - DOI - A249 Role of LRP6 in KRAS and BRAF mutated colorectal cancer - https://doi.org/10.1093/jcag/gwy009.249 - 2018 - A Côté-Biron - J Raisch - N Rivard + Waga C + Asano H + Sanagi T + Suzuki E + Nakamura Y + Tsuchiya A + Itoh M + Goto Y + Kohsaka S + Uchino S 15917271 @@ -785,103 +758,22 @@ Bertani I Bolognese F Colombo E - Caselli R - Scala E - Longo I - Grosso S - Pescucci C - Ariani F - Hayek G - Balestri P - Bergo A - Badaracco G - Zappella M - Broccoli V - 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Li Z - Wang PI - Boutz DR - Fong V - Phanse S - Babu M - Craig SA - Hu P - Wan C - Vlasblom J - Dar VU - Bezginov A - Clark GW - Wu GC - Wodak SJ - Tillier ER - Paccanaro A - Marcotte EM - Emili A + Caselli R + Scala E + Longo I + Grosso S + Pescucci C + Ariani F + Hayek G + Balestri P + Bergo A + Badaracco G + Zappella M + Broccoli V + Renieri A + Kilstrup-Nielsen C + Landsberger N - - Rett syndrome - DOID:1206 - Disease - 21931736 PubMed @@ -899,37 +791,6 @@ Mattson MP Pazin MJ - - 12437990 - PubMed - Brain-specific expression of the nuclear actin-related protein ArpNalpha and its involvement in mammalian SWI/SNF chromatin remodeling complex. - Biochem Biophys Res Commun - 2002 - Kuroda Y - Oma Y - Nishimori K - Ohta T - Harata M - - - disease pathway - PW:0000013 - Pathway Ontology - - - 23752268 - PubMed - The functional interactome landscape of the human histone deacetylase family. - Mol Syst Biol - 2013 - Joshi P - Greco TM - Guise AJ - Luo Y - Yu F - Nesvizhskii AI - Cristea IM - 26153216 PubMed @@ -954,6 +815,126 @@ Zink AM Naidu S + + 27288453 + PubMed + MeCP2 co-ordinates liver lipid metabolism with the NCoR1/HDAC3 corepressor complex. + Hum Mol Genet + 2016 + Kyle SM + Saha PK + Brown HM + Chan LC + Justice MJ + + + 23752268 + PubMed + The functional interactome landscape of the human histone deacetylase family. + Mol Syst Biol + 2013 + Joshi P + Greco TM + Guise AJ + Luo Y + Yu F + Nesvizhskii AI + Cristea IM + + + 15640247 + PubMed + CECR2, a protein involved in neurulation, forms a novel chromatin remodeling complex with SNF2L. + Hum Mol Genet + 2005 + Banting GS + Barak O + Ames TM + Burnham AC + Kardel MD + Cooch NS + Davidson CE + Godbout R + McDermid HE + Shiekhattar R + + + 22905747 + PubMed + Sodium channels and the neurobiology of epilepsy. + Epilepsia + 2012 + Oliva M + Berkovic SF + Petrou S + + + 28295012 + PubMed + Correlations between TBL1XR1 and recurrence of colorectal cancer. + Sci Rep + 2017 + Liu H + Xu Y + Zhang Q + Li K + Wang D + Li S + Ning S + Yang H + Shi W + Liu Z + Chen Y + + + Rett syndrome + DOID:1206 + Disease + + + neuron + CL:0000540 + Cell Type + + + 16464983 + PubMed + Severe epilepsy resulting from genetic interaction between Scn2a and Kcnq2. + Hum Mol Genet + 2006 + Kearney JA + Yang Y + Beyer B + Bergren SK + Claes L + Dejonghe P + Frankel WN + + + 12437990 + PubMed + Brain-specific expression of the nuclear actin-related protein ArpNalpha and its involvement in mammalian SWI/SNF chromatin remodeling complex. + Biochem Biophys Res Commun + 2002 + Kuroda Y + Oma Y + Nishimori K + Ohta T + Harata M + + + 27507650 + PubMed + Long-term potentiation modulates synaptic phosphorylation networks and reshapes the structure of the postsynaptic interactome. + Sci Signal + 2016 + Li J + Wilkinson B + Clementel VA + Hou J + O'Dell TJ + Coba MP + 17500595 PubMed @@ -982,6 +963,49 @@ Botas J Hughes RE + + 19854871 + PubMed + Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome. + RNA + 2009 + Grainger RJ + Barrass JD + Jacquier A + Rain JC + Beggs JD + + + 15136563 + PubMed + A signaling role of histone-binding proteins and INHAT subunits pp32 and Set/TAF-Ibeta in integrating chromatin hypoacetylation and transcriptional repression. + J Biol Chem + 2004 + Kutney SN + Hong R + Macfarlan T + Chakravarti D + + + 10.1093/jcag/gwy009.249 + DOI + A249 Role of LRP6 in KRAS and BRAF mutated colorectal cancer + https://doi.org/10.1093/jcag/gwy009.249 + 2018 + A Côté-Biron + J Raisch + N Rivard + + + 24662006 + PubMed + Dysregulation of the IGF-I/PI3K/AKT/mTOR signaling pathway in autism spectrum disorders. + Int J Dev Neurosci + 2014 + Chen J + Alberts I + Li X + 9620804 PubMed @@ -996,19 +1020,16 @@ Eisenman RN Bird A - - 16464983 + + 24058414 PubMed - Severe epilepsy resulting from genetic interaction between Scn2a and Kcnq2. - Hum Mol Genet - 2006 - Kearney JA - Yang Y - Beyer B - Bergren SK - Claes L - Dejonghe P - Frankel WN + Knockdown of human TCF4 affects multiple signaling pathways involved in cell survival, epithelial to mesenchymal transition and neuronal differentiation. + PLoS One + 2013 + Forrest MP + Waite AJ + Martin-Rendon E + Blake DJ 18333962 @@ -1022,27 +1043,6 @@ Tarabykin V Agoston DV - - 15752761 - PubMed - PARG1, a protein-tyrosine phosphatase-associated RhoGAP, as a putative Rap2 effector. - Biochem Biophys Res Commun - 2005 - Myagmar BE - Umikawa M - Asato T - Taira K - Oshiro M - Hino A - Takei K - Uezato H - Kariya K - - - neuron - CL:0000540 - Cell Type - diff --git a/pathways/WP4312/WP4312.json b/pathways/WP4312/WP4312.json index 6e89bb2a8..acab509ca 100644 --- a/pathways/WP4312/WP4312.json +++ b/pathways/WP4312/WP4312.json @@ -6045,7 +6045,7 @@ "id": "publicationXrefc44", "source": "Eur J Hum Genet", "standardName": "Loss-of-function variants in HIVEP2 are a cause of intellectual disability.", - "textContent": "26", + "textContent": "24", "type": [ "PublicationXref", "PubMed:26153216" @@ -6066,7 +6066,7 @@ "id": "publicationXrefc6d", "source": "Proteomics", "standardName": "Probing phosphorylation-dependent protein interactions within functional domains of histone deacetylase 5 (HDAC5).", - "textContent": "22", + "textContent": "21", "type": [ "PublicationXref", "PubMed:24920159" @@ -6091,7 +6091,7 @@ "id": "publicationXrefcba", "source": "Biochem Biophys Res Commun", "standardName": "PARG1, a protein-tyrosine phosphatase-associated RhoGAP, as a putative Rap2 effector.", - "textContent": "9", + "textContent": "7", "type": [ "PublicationXref", "PubMed:15752761" @@ -6191,7 +6191,7 @@ "id": "publicationXrefd83", "source": "Cell", "standardName": "A census of human soluble protein complexes.", - "textContent": "18", + "textContent": "17", "type": [ "PublicationXref", "PubMed:22939629" @@ -6229,7 +6229,7 @@ "id": "publicationXrefda7", "source": "Epilepsia", "standardName": "Sodium channels and the neurobiology of epilepsy.", - "textContent": "17", + "textContent": "18", "type": [ "PublicationXref", "PubMed:22905747" @@ -6268,7 +6268,7 @@ "id": "publicationXrefdce", "source": "Eur J Hum Genet", "standardName": "Atypical Rett syndrome with selective FOXG1 deletion detected by comparative genomic hybridization: case report and review of literature.", - "textContent": "14", + "textContent": "13", "type": [ "PublicationXref", "PubMed:19623215" @@ -6369,7 +6369,7 @@ "id": "publicationXreff00", "source": "Sci Signal", "standardName": "Long-term potentiation modulates synaptic phosphorylation networks and reshapes the structure of the postsynaptic interactome.", - "textContent": "24", + "textContent": "26", "type": [ "PublicationXref", "PubMed:27507650" @@ -6416,7 +6416,7 @@ "id": "publicationXreff07", "source": "J Neurochem", "standardName": "Identification of two novel Shank3 transcripts in the developing mouse neocortex.", - "textContent": "21", + "textContent": "22", "type": [ "PublicationXref", "PubMed:24164323" @@ -6442,7 +6442,7 @@ "id": "publicationXreff3b", "source": "Hum Mol Genet", "standardName": "CECR2, a protein involved in neurulation, forms a novel chromatin remodeling complex with SNF2L.", - "textContent": "7", + "textContent": "9", "type": [ "PublicationXref", "PubMed:15640247" @@ -6465,7 +6465,7 @@ "id": "publicationXreff42", "source": "Mol Syst Biol", "standardName": "The functional interactome landscape of the human histone deacetylase family.", - "textContent": "20", + "textContent": "19", "type": [ "PublicationXref", "PubMed:23752268" @@ -6506,7 +6506,7 @@ "id": "publicationXreffb9", "source": "Cell Adh Migr", "standardName": "Huntingtin associated protein 1 and its functions.", - "textContent": "13", + "textContent": "14", "type": [ "PublicationXref", "PubMed:19262167" @@ -6526,7 +6526,7 @@ "id": "publicationXreffdb", "source": "PLoS One", "standardName": "Knockdown of human TCF4 affects multiple signaling pathways involved in cell survival, epithelial to mesenchymal transition and neuronal differentiation.", - "textContent": "19", + "textContent": "20", "type": [ "PublicationXref", "PubMed:24058414" diff --git a/pathways/WP4364/WP4364.gpml b/pathways/WP4364/WP4364.gpml index 0428a94ce..ad3c80a6b 100644 --- a/pathways/WP4364/WP4364.gpml +++ b/pathways/WP4364/WP4364.gpml @@ -1033,23 +1033,30 @@ Expresses in seed and is involved in XA21 mediated immunity and submergence tole - - stress response pathway - PW:0000237 - Pathway Ontology - - - 18273684 + + 25445270 PubMed - Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice. - Plant Mol Biol - 2008 - Hu H - You J - Fang Y - Zhu X - Qi Z - Xiong L + Synergistic regulatory networks mediated by microRNAs and transcription factors under drought, heat and salt stresses in Oryza Sativa spp. + Gene + 2015 + Nigam D + Kumar S + Mishra DC + Rai A + Smita S + Saha A + + + 24894389 + PubMed + Metabolic and transcriptional regulatory mechanisms underlying the anoxic adaptation of rice coleoptile. + AoB Plants + 2014 + Lakshmanan M + Mohanty B + Lim SH + Ha SH + Lee DY 21533176 @@ -1079,18 +1086,57 @@ Expresses in seed and is involved in XA21 mediated immunity and submergence tole Jeon JS Ronald PC - - 23010196 + + 20335401 PubMed - Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice. - Gene - 2012 - Mohanty B - Herath V - Wijaya E - Yeo HC - de Los Reyes BG - Lee DY + Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. + Plant Physiol + 2010 + Jeong JS + Kim YS + Baek KH + Jung H + Ha SH + Do Choi Y + Kim M + Reuzeau C + Kim JK + + + 18583533 + PubMed + An abscisic acid-induced protein, HVA22, inhibits gibberellin-mediated programmed cell death in cereal aleurone cells. + Plant Physiol + 2008 + Guo WJ + Ho TH + + + 23581288 + PubMed + The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism. + Plant J + 2013 + Guo X + Hou X + Fang J + Wei P + Xu B + Chen M + Feng Y + Chu C + + + 23620302 + PubMed + Abiotic stress responsive rice ASR1 and ASR3 exhibit different tissue-dependent sugar and hormone-sensitivities. + Mol Cells + 2013 + Joo J + Lee YH + Kim YK + Nahm BH + Song SI 20039193 @@ -1109,31 +1155,51 @@ Expresses in seed and is involved in XA21 mediated immunity and submergence tole An G Park PB - - 23620302 + + 24280312 PubMed - Abiotic stress responsive rice ASR1 and ASR3 exhibit different tissue-dependent sugar and hormone-sensitivities. - Mol Cells + WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. + Rice (N Y) 2013 - Joo J - Lee YH - Kim YK - Nahm BH - Song SI + Hanumappa M + Preece J + Elser J + Nemeth D + Bono G + Wu K + Jaiswal P - - 25445270 + + 24782137 PubMed - Synergistic regulatory networks mediated by microRNAs and transcription factors under drought, heat and salt stresses in Oryza Sativa spp. - Gene - 2015 - Nigam D - Kumar S - Mishra DC - Rai A - Smita S - Saha A + Mini review roles of the bZIP gene family in rice. + Genet Mol Res + 2014 + E ZG + Zhang YP + Zhou JH + Wang L + + + 20632034 + PubMed + The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. + Mol Genet Genomics + 2010 + Takasaki H + Maruyama K + Kidokoro S + Ito Y + Fujita Y + Shinozaki K + Yamaguchi-Shinozaki K + Nakashima K + + stress response pathway + PW:0000237 + Pathway Ontology + 26706071 PubMed @@ -1151,32 +1217,68 @@ Expresses in seed and is involved in XA21 mediated immunity and submergence tole Choi YD Kim JK - - 24782137 + + 26566840 PubMed - Mini review roles of the bZIP gene family in rice. - Genet Mol Res + Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network. + Plant Sci + 2016 + Mohanty B + Kitazumi A + Cheung CY + Lakshmanan M + de Los Reyes BG + Jang IC + Lee DY + + + 25445270 + PubMed + Synergistic regulatory networks mediated by microRNAs and transcription factors under drought, heat and salt stresses in Oryza Sativa spp. + Gene + 2015 + Nigam D + Kumar S + Mishra DC + Rai A + Smita S + Saha A + + + 25428615 + PubMed + Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress. + BMC Genomics 2014 - E ZG - Zhang YP - Zhou JH - Wang L + Huang L + Zhang F + Wang W + Zhou Y + Fu B + Li Z - - 20335401 + + 23010196 PubMed - Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. - Plant Physiol - 2010 - Jeong JS - Kim YS - Baek KH - Jung H - Ha SH - Do Choi Y - Kim M - Reuzeau C - Kim JK + Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice. + Gene + 2012 + Mohanty B + Herath V + Wijaya E + Yeo HC + de Los Reyes BG + Lee DY + + + 25741357 + PubMed + Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants. + Front Plant Sci + 2015 + Todaka D + Shinozaki K + Yamaguchi-Shinozaki K 16924117 @@ -1192,28 +1294,23 @@ Expresses in seed and is involved in XA21 mediated immunity and submergence tole Zhang Q Xiong L - - 24280312 - PubMed - WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. - Rice (N Y) - 2013 - Hanumappa M - Preece J - Elser J - Nemeth D - Bono G - Wu K - Jaiswal P - - - 18583533 + + signaling pathway + PW:0000003 + Pathway Ontology + + + 18273684 PubMed - An abscisic acid-induced protein, HVA22, inhibits gibberellin-mediated programmed cell death in cereal aleurone cells. - Plant Physiol + Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice. + Plant Mol Biol 2008 - Guo WJ - Ho TH + Hu H + You J + Fang Y + Zhu X + Qi Z + Xiong L @@ -1228,33 +1325,29 @@ Expresses in seed and is involved in XA21 mediated immunity and submergence tole Hirasawa T Kanekatsu M - - 25428615 + + 23948082 PubMed - Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress. - BMC Genomics - 2014 - Huang L - Zhang F - Wang W - Zhou Y - Fu B - Li Z + Genome-wide analysis of endosperm-specific genes in rice. + Gene + 2013 + Nie DM + Ouyang YD + Wang X + Zhou W + Hu CG + Yao J - - 20632034 + + 25106855 PubMed - The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. - Mol Genet Genomics - 2010 - Takasaki H - Maruyama K - Kidokoro S - Ito Y - Fujita Y - Shinozaki K - Yamaguchi-Shinozaki K - Nakashima K + The rice WUSCHEL-related homeobox genes are involved in reproductive organ development, hormone signaling and abiotic stress response. + Gene + 2014 + Cheng S + Huang Y + Zhu N + Zhao Y 20100339 @@ -1273,18 +1366,6 @@ Expresses in seed and is involved in XA21 mediated immunity and submergence tole Bruskiewich R de Los Reyes BG - - 24894389 - PubMed - Metabolic and transcriptional regulatory mechanisms underlying the anoxic adaptation of rice coleoptile. - AoB Plants - 2014 - Lakshmanan M - Mohanty B - Lim SH - Ha SH - Lee DY - 19539489 PubMed @@ -1297,87 +1378,6 @@ Expresses in seed and is involved in XA21 mediated immunity and submergence tole Singh A Grover A - - 25445270 - PubMed - Synergistic regulatory networks mediated by microRNAs and transcription factors under drought, heat and salt stresses in Oryza Sativa spp. - Gene - 2015 - Nigam D - Kumar S - Mishra DC - Rai A - Smita S - Saha A - - - signaling pathway - PW:0000003 - Pathway Ontology - - - 26566840 - PubMed - Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network. - Plant Sci - 2016 - Mohanty B - Kitazumi A - Cheung CY - Lakshmanan M - de Los Reyes BG - Jang IC - Lee DY - - - 25106855 - PubMed - The rice WUSCHEL-related homeobox genes are involved in reproductive organ development, hormone signaling and abiotic stress response. - Gene - 2014 - Cheng S - Huang Y - Zhu N - Zhao Y - - - 23581288 - PubMed - The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism. - Plant J - 2013 - Guo X - Hou X - Fang J - Wei P - Xu B - Chen M - Feng Y - Chu C - - - 23948082 - PubMed - Genome-wide analysis of endosperm-specific genes in rice. - Gene - 2013 - Nie DM - Ouyang YD - Wang X - Zhou W - Hu CG - Yao J - - - 25741357 - PubMed - Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants. - Front Plant Sci - 2015 - Todaka D - Shinozaki K - Yamaguchi-Shinozaki K - diff --git a/pathways/WP4364/WP4364.json b/pathways/WP4364/WP4364.json index e1b35e379..e13e7471c 100644 --- a/pathways/WP4364/WP4364.json +++ b/pathways/WP4364/WP4364.json @@ -8414,7 +8414,7 @@ "id": "publicationXrefa5a", "source": "Mol Cells", "standardName": "Abiotic stress responsive rice ASR1 and ASR3 exhibit different tissue-dependent sugar and hormone-sensitivities.", - "textContent": "11", + "textContent": "12", "type": [ "PublicationXref", "PubMed:23620302" @@ -8514,7 +8514,7 @@ "id": "publicationXrefb3b", "source": "AoB Plants", "standardName": "Metabolic and transcriptional regulatory mechanisms underlying the anoxic adaptation of rice coleoptile.", - "textContent": "18", + "textContent": "16", "type": [ "PublicationXref", "PubMed:24894389" @@ -8551,7 +8551,7 @@ "id": "publicationXrefcb4", "source": "Plant Physiol", "standardName": "An abscisic acid-induced protein, HVA22, inhibits gibberellin-mediated programmed cell death in cereal aleurone cells.", - "textContent": "3", + "textContent": "2", "type": [ "PublicationXref", "PubMed:18583533" @@ -8577,7 +8577,7 @@ "id": "publicationXrefcfc", "source": "Plant Mol Biol", "standardName": "The bZIP transcription factor OsABF1 is an ABA responsive element binding factor that enhances abiotic stress signaling in rice.", - "textContent": "5", + "textContent": "6", "type": [ "PublicationXref", "PubMed:20039193" @@ -8600,7 +8600,7 @@ "id": "publicationXrefd12", "source": "Rice (N Y)", "standardName": "WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks.", - "textContent": "12", + "textContent": "13", "type": [ "PublicationXref", "PubMed:24280312" @@ -8641,7 +8641,7 @@ "id": "publicationXrefd61", "source": "Genet Mol Res", "standardName": "Mini review roles of the bZIP gene family in rice.", - "textContent": "16", + "textContent": "17", "type": [ "PublicationXref", "PubMed:24782137" @@ -8759,7 +8759,7 @@ "id": "publicationXrefdd0", "source": "BMC Genomics", "standardName": "Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress.", - "textContent": "17", + "textContent": "18", "type": [ "PublicationXref", "PubMed:25428615" @@ -8804,7 +8804,7 @@ "id": "publicationXrefdeb", "source": "Plant Mol Biol", "standardName": "Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice.", - "textContent": "2", + "textContent": "3", "type": [ "PublicationXref", "PubMed:18273684" @@ -8826,7 +8826,7 @@ "id": "publicationXrefdfc", "source": "Plant Biotechnology", "standardName": "Proteomic analysis of stress-related proteins in rice seeds during the desiccation phase of grain filling", - "textContent": "13", + "textContent": "14", "type": [ "PublicationXref" ], @@ -8896,7 +8896,7 @@ "id": "publicationXrefea7", "source": "Plant Physiol", "standardName": "Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions.", - "textContent": "6", + "textContent": "5", "type": [ "PublicationXref", "PubMed:20335401" @@ -8920,7 +8920,7 @@ "id": "publicationXreff2e", "source": "Plant J", "standardName": "The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism.", - "textContent": "14", + "textContent": "11", "type": [ "PublicationXref", "PubMed:23581288" diff --git a/pathways/WP4523/WP4523.gpml b/pathways/WP4523/WP4523.gpml index 8eace9773..8a7530fd3 100644 --- a/pathways/WP4523/WP4523.gpml +++ b/pathways/WP4523/WP4523.gpml @@ -1220,88 +1220,74 @@ Mineralocorticoid (M) and glucocorticoid (G) receptors regulate transcription; e - - 21325058 + + 27068427 PubMed - Cortisone-reductase deficiency associated with heterozygous mutations in 11beta-hydroxysteroid dehydrogenase type 1. - Proc Natl Acad Sci U S A - 2011 - Lawson AJ - Walker EA - Lavery GG - Bujalska IJ - Hughes B - Arlt W - Stewart PM - Ride JP + P450 Oxidoreductase deficiency: Analysis of mutations and polymorphisms. + J Steroid Biochem Mol Biol + 2017 + Burkhard FZ + Parween S + Udhane SS + Flück CE + Pandey AV - - 29553041 + + 16216911 PubMed - Aromatase Deficiency due to a Novel Mutation in<i>CYP19A1</i>Gene - J Clin Res Pediatr Endocrinol - 2018 - Unal E - TaÅŸ FF - Demir V - Onay H - Haspolat YK + Androgen metabolism via 17beta-hydroxysteroid dehydrogenase type 3 in mammalian and non-mammalian vertebrates: comparison of the human and the zebrafish enzyme. + J Mol Endocrinol + 2005 + Mindnich R + Haller F + Halbach F + Moeller G + Hrabé de Angelis M + Adamski J - - 10898110 + + 1594605 PubMed - Biochemical and pharmacogenetic dissection of human steroid 5 alpha-reductase type II. - Pharmacogenetics - 2000 - Makridakis NM - di Salle E - Reichardt JK + Mutations in the human CYP11B2 (aldosterone synthase) gene causing corticosterone methyloxidase II deficiency. + Proc Natl Acad Sci U S A + 1992 + Pascoe L + Curnow KM + Slutsker L + Rösler A + White PC - congenital adrenal hyperplasia - DOID:0050811 - Disease - - - apparent mineralocorticoid excess syndrome - DOID:4367 + cortisone reductase deficiency + DOID:0090139 Disease - - 24790347 + + 27163392 PubMed - Cholesterol Side-Chain Cleavage Enzyme (SCC) Deficiency. - Clin Pediatr Endocrinol - 2007 - Katsumata N + 46,XY disorder of sex development (DSD) due to 17β-hydroxysteroid dehydrogenase type 3 deficiency. + J Steroid Biochem Mol Biol + 2017 + Mendonca BB + Gomes NL + Costa EM + Inacio M + Martin RM + Nishi MY + Carvalho FM + Tibor FD + Domenice S - apparent mineralocorticoid excess - DOID:0090121 + lipoid congenital adrenal hyperplasia pathway + PW:0001479 + Pathway Ontology + + + congenital adrenal hyperplasia + DOID:0050811 Disease - - 8001864 - PubMed - [The importance of DNA analysis in the diagnosis of steroid 5-alpha-reductase deficiency]. - Ginekol Pol - 1994 - Kostyrko A - Antkowiak J - Warenik-Szymankiewicz A - Trzeciak WH - - - 19129847 - PubMed - Structural basis for androgen specificity and oestrogen synthesis in human aromatase. - Nature - 2009 - Ghosh D - Griswold J - Erman M - Pangborn W - 21636783 PubMed @@ -1315,50 +1301,71 @@ Mineralocorticoid (M) and glucocorticoid (G) receptors regulate transcription; e Usanov S Park HW - - apparent mineralocorticoid excess syndrome pathway - PW:0002466 - Pathway Ontology - - - 29224098 + + 28423456 PubMed - Role of Estrogens in the Regulation of Liver Lipid Metabolism. - Adv Exp Med Biol + Progesterone resistance in endometriosis: origins, consequences and interventions. + Acta Obstet Gynecol Scand 2017 - Palmisano BT - Zhu L - Stafford JM + Patel BG + Rudnicki M + Yu J + Shu Y + Taylor RN + + + 13211659 + PubMed + On the mechanism of the C11 beta-hydroxylation of steroids. + J Biol Chem + 1954 + HAYANO M + DORFMAN RI + + + 26956190 + PubMed + Apparent mineralocorticoid excess. + J Steroid Biochem Mol Biol + 2017 + Funder JW - congenital adrenal hyperplasia pathway - PW:0001478 + steroid biosynthetic pathway + PW:0001152 Pathway Ontology - - 16024935 + + disease pathway + PW:0000013 + Pathway Ontology + + + 29553041 PubMed - Steroid 11-beta-hydroxylase deficiency caused by compound heterozygosity for a novel mutation, p.G314R, in one CYP11B1 allele, and a chimeric CYP11B2/CYP11B1 in the other allele. - Horm Res - 2005 - Kuribayashi I - Nomoto S - Massa G - Oostdijk W - Wit JM - Wolffenbuttel BH - Shizuta Y - Honke K + Aromatase Deficiency due to a Novel Mutation in<i>CYP19A1</i>Gene + J Clin Res Pediatr Endocrinol + 2018 + Unal E + TaÅŸ FF + Demir V + Onay H + Haspolat YK - - 27380651 + + 8839934 PubMed - Steroid 21-hydroxylase deficiency in congenital adrenal hyperplasia. - J Steroid Biochem Mol Biol - 2017 - Parsa AA - New MI + Molecular biology of mineralocorticoid metabolism. + Annu Rev Nutr + 1996 + Fardella CE + Miller WL + + apparent mineralocorticoid excess + DOID:0090121 + Disease + 9405715 PubMed @@ -1377,23 +1384,15 @@ Mineralocorticoid (M) and glucocorticoid (G) receptors regulate transcription; e Seckl JR Mullins JJ - - 26956190 - PubMed - Apparent mineralocorticoid excess. - J Steroid Biochem Mol Biol - 2017 - Funder JW - - - 27047663 + + 10898110 PubMed - Lipoid congenital adrenal hyperplasia due to STAR mutations in a Caucasian patient. - Endocrinol Diabetes Metab Case Rep - 2016 - Kaur J - Casas L - Bose HS + Biochemical and pharmacogenetic dissection of human steroid 5 alpha-reductase type II. + Pharmacogenetics + 2000 + Makridakis NM + di Salle E + Reichardt JK 12788846 @@ -1414,24 +1413,47 @@ Mineralocorticoid (M) and glucocorticoid (G) receptors regulate transcription; e Montero JA Fardella CE - - 26161337 + + 16024935 PubMed - A case of 17 alpha-hydroxylase deficiency. - Clin Exp Reprod Med - 2015 - Kim SM - Rhee JH + Steroid 11-beta-hydroxylase deficiency caused by compound heterozygosity for a novel mutation, p.G314R, in one CYP11B1 allele, and a chimeric CYP11B2/CYP11B1 in the other allele. + Horm Res + 2005 + Kuribayashi I + Nomoto S + Massa G + Oostdijk W + Wit JM + Wolffenbuttel BH + Shizuta Y + Honke K - - 13211659 + + 24790347 PubMed - On the mechanism of the C11 beta-hydroxylation of steroids. - J Biol Chem - 1954 - HAYANO M - DORFMAN RI + Cholesterol Side-Chain Cleavage Enzyme (SCC) Deficiency. + Clin Pediatr Endocrinol + 2007 + Katsumata N + + + 7697895 + PubMed + Corticosterone methyl oxidase type II (CMO II) deficiency: biochemical approach to diagnosis. + Clin Biochem + 1994 + Yong AB + Montalto J + Pitt J + Oakes S + Preston T + Buchanan C + + pseudohermaphroditism + DOID:3765 + Disease + 25322271 PubMed @@ -1449,11 +1471,75 @@ Mineralocorticoid (M) and glucocorticoid (G) receptors regulate transcription; e Rivarola MA Belgorosky A + + classic metabolic pathway + PW:0000002 + Pathway Ontology + + + C19-steroid hormone biosynthetic pathway + PW:0000770 + Pathway Ontology + + + 27380651 + PubMed + Steroid 21-hydroxylase deficiency in congenital adrenal hyperplasia. + J Steroid Biochem Mol Biol + 2017 + Parsa AA + New MI + + + 26161337 + PubMed + A case of 17 alpha-hydroxylase deficiency. + Clin Exp Reprod Med + 2015 + Kim SM + Rhee JH + + + 29224098 + PubMed + Role of Estrogens in the Regulation of Liver Lipid Metabolism. + Adv Exp Med Biol + 2017 + Palmisano BT + Zhu L + Stafford JM + congenital adrenal insufficiency DOID:0050546 Disease + + 8001864 + PubMed + [The importance of DNA analysis in the diagnosis of steroid 5-alpha-reductase deficiency]. + Ginekol Pol + 1994 + Kostyrko A + Antkowiak J + Warenik-Szymankiewicz A + Trzeciak WH + + + 21325058 + PubMed + Cortisone-reductase deficiency associated with heterozygous mutations in 11beta-hydroxysteroid dehydrogenase type 1. + Proc Natl Acad Sci U S A + 2011 + Lawson AJ + Walker EA + Lavery GG + Bujalska IJ + Hughes B + Arlt W + Stewart PM + Ride JP + 9783642403361 ISBN @@ -1469,71 +1555,37 @@ Mineralocorticoid (M) and glucocorticoid (G) receptors regulate transcription; e Dionisi-Vici Carlo - 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C19-steroid hormone biosynthetic pathway - PW:0000770 + apparent mineralocorticoid excess syndrome pathway + PW:0002466 Pathway Ontology - - 7697895 - PubMed - Corticosterone methyl oxidase type II (CMO II) deficiency: biochemical approach to diagnosis. - Clin Biochem - 1994 - Yong AB - Montalto J - Pitt J - Oakes S - Preston T - Buchanan C - + + apparent mineralocorticoid excess syndrome + DOID:4367 + Disease + 9046958 PubMed @@ -1542,57 +1594,20 @@ Mineralocorticoid (M) and glucocorticoid (G) receptors regulate transcription; e 1997 Funder JW - - 8839934 - PubMed - Molecular biology of mineralocorticoid metabolism. - Annu Rev Nutr - 1996 - Fardella CE - Miller WL - - - 28423456 - PubMed - Progesterone resistance in endometriosis: origins, consequences and interventions. - Acta Obstet Gynecol Scand - 2017 - Patel BG - Rudnicki M - Yu J - Shu Y - Taylor RN - - - pseudohermaphroditism - DOID:3765 - Disease - - C21-steroid hormone biosynthetic pathway - PW:0000070 - Pathway Ontology - - - disease pathway - PW:0000013 + glucocorticoid biosynthetic pathway + PW:0000772 Pathway Ontology - - 27163392 + + 27047663 PubMed - 46,XY disorder of sex development (DSD) due to 17β-hydroxysteroid dehydrogenase type 3 deficiency. - J Steroid Biochem Mol Biol - 2017 - Mendonca BB - Gomes NL - Costa EM - Inacio M - Martin RM - Nishi MY - Carvalho FM - Tibor FD - Domenice S + Lipoid congenital adrenal hyperplasia due to STAR mutations in a Caucasian patient. + Endocrinol Diabetes Metab Case Rep + 2016 + Kaur J + Casas L + Bose HS 12050213 @@ -1611,21 +1626,6 @@ Mineralocorticoid (M) and glucocorticoid (G) receptors regulate transcription; e Smillie KJ Mason JI - - classic metabolic pathway - PW:0000002 - Pathway Ontology - - - cortisone reductase deficiency - DOID:0090139 - Disease - - - steroid biosynthetic pathway - PW:0001152 - Pathway Ontology - diff --git a/pathways/WP4523/WP4523.json b/pathways/WP4523/WP4523.json index 0011f6b20..89d52040b 100644 --- a/pathways/WP4523/WP4523.json +++ b/pathways/WP4523/WP4523.json @@ -11744,7 +11744,7 @@ "id": "publicationXrefb84", "source": "Ginekol Pol", "standardName": "[The importance of DNA analysis in the diagnosis of steroid 5-alpha-reductase deficiency].", - "textContent": "3", + "textContent": "4", "type": [ "PublicationXref", "PubMed:8001864" @@ -11814,7 +11814,7 @@ "id": "publicationXrefc44", "source": "J Steroid Biochem Mol Biol", "standardName": "46,XY disorder of sex development (DSD) due to 17β-hydroxysteroid dehydrogenase type 3 deficiency.", - "textContent": "26", + "textContent": "22", "type": [ "PublicationXref", "PubMed:27163392" @@ -11833,7 +11833,7 @@ "id": "publicationXrefc51", "source": "Adv Exp Med Biol", "standardName": "Role of Estrogens in the Regulation of Liver Lipid Metabolism.", - "textContent": "21", + "textContent": "26", "type": [ "PublicationXref", "PubMed:29224098" @@ -11854,7 +11854,7 @@ "id": "publicationXrefc94", "source": "Acta Obstet Gynecol Scand", "standardName": "Progesterone resistance in endometriosis: origins, consequences and interventions.", - "textContent": "25", + "textContent": "23", "type": [ "PublicationXref", "PubMed:28423456" @@ -11893,7 +11893,7 @@ "id": "publicationXrefcca", "source": "J Steroid Biochem Mol Biol", "standardName": "Steroid 21-hydroxylase deficiency in congenital adrenal hyperplasia.", - "textContent": "22", + "textContent": "25", "type": [ "PublicationXref", "PubMed:27380651" @@ -11936,7 +11936,7 @@ "id": "publicationXrefd31", "source": "Horm Res", "standardName": "Steroid 11-beta-hydroxylase deficiency caused by compound heterozygosity for a novel mutation, p.G314R, in one CYP11B1 allele, and a chimeric CYP11B2/CYP11B1 in the other allele.", - "textContent": "11", + "textContent": "12", "type": [ "PublicationXref", "PubMed:16024935" @@ -11960,7 +11960,7 @@ "id": "publicationXrefd46", "source": "Proc Natl Acad Sci U S A", "standardName": "Cortisone-reductase deficiency associated with heterozygous mutations in 11beta-hydroxysteroid dehydrogenase type 1.", - "textContent": "15", + "textContent": "16", "type": [ "PublicationXref", "PubMed:21325058" @@ -12003,7 +12003,7 @@ "id": "publicationXrefdf7", "source": "Clin Biochem", "standardName": "Corticosterone methyl oxidase type II (CMO II) deficiency: biochemical approach to diagnosis.", - "textContent": "4", + "textContent": "3", "type": [ "PublicationXref", "PubMed:7697895" @@ -12042,7 +12042,7 @@ "id": "publicationXrefe17", "source": "J Steroid Biochem Mol Biol", "standardName": "P450 Oxidoreductase deficiency: Analysis of mutations and polymorphisms.", - "textContent": "24", + "textContent": "21", "type": [ "PublicationXref", "PubMed:27068427" @@ -12064,7 +12064,7 @@ "id": "publicationXrefe30", "source": "Proc Natl Acad Sci U S A", "standardName": "Structural basis for pregnenolone biosynthesis by the mitochondrial monooxygenase system.", - "textContent": "16", + "textContent": "15", "type": [ "PublicationXref", "PubMed:21636783" @@ -12086,7 +12086,7 @@ "id": "publicationXrefe35", "source": "J Mol Endocrinol", "standardName": "Androgen metabolism via 17beta-hydroxysteroid dehydrogenase type 3 in mammalian and non-mammalian vertebrates: comparison of the human and the zebrafish enzyme.", - "textContent": "12", + "textContent": "11", "type": [ "PublicationXref", "PubMed:16216911" @@ -12121,7 +12121,7 @@ "id": "publicationXreff13", "source": "Clin Exp Reprod Med", "standardName": "A case of 17 alpha-hydroxylase deficiency.", - "textContent": "18", + "textContent": "19", "type": [ "PublicationXref", "PubMed:26161337" @@ -12186,7 +12186,7 @@ "id": "publicationXreff8a", "source": "J Steroid Biochem Mol Biol", "standardName": "Apparent mineralocorticoid excess.", - "textContent": "23", + "textContent": "24", "type": [ "PublicationXref", "PubMed:26956190" @@ -12212,7 +12212,7 @@ "id": "publicationXrefff1", "source": "J Clin Endocrinol Metab", "standardName": "A novel missense mutation in the HSD3B2 gene, underlying nonsalt-wasting congenital adrenal hyperplasia. new insight into the structure-function relationships of 3β-hydroxysteroid dehidrogenase type II.", - "textContent": "19", + "textContent": "18", "type": [ "PublicationXref", "PubMed:25322271" @@ -12479,15 +12479,15 @@ "textContent": "Name: Classical pathway of steroidogenesis with glucocorticoid and mineralocorticoid metabolism\nLast Modified: 20240720124004\nOrganism: Homo sapiens", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0002466", - "http://identifiers.org/pw/PW:0001478", "http://identifiers.org/pw/PW:0001479", - "http://identifiers.org/pw/PW:0000772", - "http://identifiers.org/pw/PW:0000770", - "http://identifiers.org/pw/PW:0000070", + "http://identifiers.org/pw/PW:0001152", "http://identifiers.org/pw/PW:0000013", "http://identifiers.org/pw/PW:0000002", - "http://identifiers.org/pw/PW:0001152" + "http://identifiers.org/pw/PW:0000770", + "http://identifiers.org/pw/PW:0001478", + "http://identifiers.org/pw/PW:0000070", + "http://identifiers.org/pw/PW:0002466", + "http://identifiers.org/pw/PW:0000772" ], "verticalAlign": "top", "width": 1602.7777777777767, diff --git a/pathways/WP4549/WP4549.gpml b/pathways/WP4549/WP4549.gpml index 336afc0ef..b574eeb81 100644 --- a/pathways/WP4549/WP4549.gpml +++ b/pathways/WP4549/WP4549.gpml @@ -3599,39 +3599,14 @@ protein (CREB) at Ser133 - - 16055064 - PubMed - PICK1 interacts with ABP/GRIP to regulate AMPA receptor trafficking. - Neuron - 2005 - Lu W - Ziff EB - - - 17644144 + + 27847432 PubMed - Regulation of NMDA receptors by phosphorylation. - Neuropharmacology - 2007 - Chen BS - Roche KW - - - 10.1186/2040-2392-5-16 - DOI - Divergent dysregulation of gene expression in murine models of fragile X syndrome and tuberous sclerosis - https://doi.org/10.1186/2040-2392-5-16 - 2014 - Kong, Sek Won - Mustafa Sahin - 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Landreth + + + 18474609 + PubMed + S6K1 phosphorylates and regulates fragile X mental retardation protein (FMRP) with the neuronal protein synthesis-dependent mammalian target of rapamycin (mTOR) signaling cascade. + J Biol Chem + 2008 + Narayanan U + Nalavadi V + Nakamoto M + Thomas G Ceman S - O'Donnell WT - Reed M - Patton S - Pohl J + Bassell GJ Warren ST - - 19345194 + + 27573877 PubMed - The postsynaptic density proteins Homer and Shank form a polymeric network structure. - Cell - 2009 - Hayashi MK - Tang C - Verpelli C - Narayanan R - Stearns MH - Xu RM - Li H - Sala C - Hayashi Y + Novel roles of amyloid-beta precursor protein metabolites in fragile X syndrome and autism. + Mol Psychiatry + 2016 + Westmark CJ + Sokol DK + Maloney B + Lahiri DK - - 29410531 + + 20410124 PubMed - Mechanisms of clathrin-mediated endocytosis - Nature - 2018 - Marko Kaksonen - Aurélien Roux + Enhanced endocannabinoid signaling elevates neuronal excitability in fragile X syndrome. + J Neurosci + 2010 + Zhang L + Alger BE - - 28859574 + + 27889578 PubMed - Cognitive Dysfunctions in Intellectual Disabilities: The Contributions of the Ras-MAPK and PI3K-AKT-mTOR Pathways. - Annu Rev Genomics Hum Genet + Molecular Neurobiology of mTOR + Google Scholar 2017 - Borrie SC - Brems H - Legius E - Bagni C + Katarzyna Switona + Katarzyna Kotulskab + Aleksandra Janusz-Kaminskaa + Justyna Zmorzynskaa + Jacek Jaworski 14585353 @@ -4192,50 +4121,30 @@ protein (CREB) at Ser133 Manning BD Cantley LC - - 22483044 - PubMed - The pathophysiology of fragile X (and what it teaches us about synapses). - Annu Rev Neurosci - 2012 - Bhakar AL - Dölen G - Bear MF - - - 24727796 - PubMed - FMRP regulates miR196a-mediated repression of HOXB8 via interaction with the AGO2 MID domain. - Mol Biosyst - 2014 - Li Y - Tang W - Zhang LR - Zhang CY - - - 30447757 + + 28473628 PubMed - ERK/MAPK signaling and autism spectrum disorders - ScienceDirect - 2018 - Joseph Vithayathil - Joanna Pucilowska - Gary E. Landreth + Molecular mechanisms of Dicer: endonuclease and enzymatic activity. + Biochem J + 2017 + Song MS + Rossi JJ - - 27239350 + + 17088211 PubMed - Synaptic Plasticity, a Prominent Contributor to the Anxiety in Fragile X Syndrome. - Neural Plast - 2016 - Yang T - Zhao H - Lu C - Li X - Xie Y - Fu H - Xu H + Arc/Arg3.1 interacts with the endocytic machinery to regulate AMPA receptor trafficking. + Neuron + 2006 + Chowdhury S + Shepherd JD + Okuno H + Lyford G + Petralia RS + Plath N + Kuhl D + Huganir RL + Worley PF 25729352 @@ -4245,44 +4154,87 @@ protein (CREB) at Ser133 2015 Hansen Wang - - 24533017 + + 19436069 PubMed - The role of ionotropic glutamate receptors in childhood neurodevelopmental disorders: autism spectrum disorders and fragile x syndrome. - Curr Neuropharmacol - 2014 - Uzunova G - Hollander E - Shepherd J + Ca2+/calmodulin-dependent protein kinase IV links group I metabotropic glutamate receptors to fragile X mental retardation protein in cingulate cortex. + J Biol Chem + 2009 + Wang H + Fukushima H + Kida S + Zhuo M - - 30705620 + + 30364226 PubMed - Fragile-X Syndrome Is Associated With NMDA Receptor Hypofunction and Reduced Dendritic Complexity in Mature Dentate Granule Cells. - Front Mol Neurosci + The Regulation of AMPA Receptor Endocytosis by Dynamic Protein-Protein Interactions. + Front Cell Neurosci 2018 - Yau SY - Bettio L - Chiu J - Chiu C - Christie BR + Hanley JG - - 20186705 + + 22267161 PubMed - Postsynaptic BDNF-TrkB signaling in synapse maturation, plasticity, and disease. - Dev Neurobiol - 2010 - Yoshii A - Constantine-Paton M + Disrupted Homer scaffolds mediate abnormal mGluR5 function in a mouse model of fragile X syndrome. + Nat Neurosci + 2012 + Ronesi JA + Collins KA + Hays SA + Tsai NP + Guo W + Birnbaum SG + Hu JH + Worley PF + Gibson JR + Huber KM - - 9839441 + + 25113167 PubMed - Fyn, a Src family tyrosine kinase. - Int J Biochem Cell Biol - 1998 - Resh MD + Activity-dependent alterations in the sensitivity to BDNF-TrkB signaling may promote excessive dendritic arborization and spinogenesis in fragile X syndrome in order to compensate for compromised postsynaptic activity. + Med Hypotheses + 2014 + Kim SW + Cho KJ + + + 18332424 + PubMed + Aberrant early-phase ERK inactivation impedes neuronal function in fragile X syndrome. + Proc Natl Acad Sci U S A + 2008 + Kim SH + Markham JA + Weiler IJ + Greenough WT + + + 12563289 + PubMed + Tor signalling in bugs, brain and brawn. + Nat Rev Mol Cell Biol + 2003 + Jacinto E + Hall MN + + + 10.5451/unibas-003209151 + DOI + Analysis of the Structure and Function of Protein Phosphatase 2A + http://edoc.unibas.ch/diss/DissB_6695; Institutional Repository of the University of Basel + 2004 + Karsten Schmidt + + + 17298186 + PubMed + FMRP mediates mGluR5-dependent translation of amyloid precursor protein. + PLoS Biol + 2007 + Westmark CJ + Malter JS 24346713 @@ -4294,14 +4246,27 @@ protein (CREB) at Ser133 Moon C Wang H - - 12563289 + + 30686771 PubMed - Tor signalling in bugs, brain and brawn. - Nat Rev Mol Cell Biol - 2003 - Jacinto E - Hall MN + The translational regulator FMRP controls lipid and glucose metabolism in mice and humans. + Mol Metab + 2019 + Leboucher A + Pisani DF + Martinez-Gili L + Chilloux J + Bermudez-Martin P + Van Dijck A + Ganief T + Macek B + Becker JAJ + Le Merrer J + Kooy RF + Amri EZ + Khandjian EW + Dumas ME + Davidovic L 22510460 @@ -4312,73 +4277,125 @@ protein (CREB) at Ser133 Lüscher C Malenka RC + + 27257628 + PubMed + Activity-Regulated Cytoskeleton-Associated Protein Controls AMPAR Endocytosis through a Direct Interaction with Clathrin-Adaptor Protein 2. + eNeuro + 2016 + DaSilva LL + Wall MJ + P de Almeida L + Wauters SC + Januário YC + Müller J + Corrêa SA + + + 29410531 + PubMed + Mechanisms of clathrin-mediated endocytosis + Nature + 2018 + Marko Kaksonen + Aurélien Roux + + + 16939974 + PubMed + Neurotrophin-regulated signalling pathways + Philos Trans R Soc Lond B Biol Sci + 2006 + LF Reichard + + + 22483044 + PubMed + The pathophysiology of fragile X (and what it teaches us about synapses). + Annu Rev Neurosci + 2012 + Bhakar AL + Dölen G + Bear MF + fragile X syndrome DOID:14261 Disease - - 22267161 + + 19345194 + PubMed + The postsynaptic density proteins Homer and Shank form a polymericnetwork structure. + Cell + 2009 + Hayashi MK + Tang C + Verpelli C + Narayanan R + Stearns MH + Xu RM + Li H + Sala C + Hayashi Y + + + 16125054 + PubMed + The cAMP signalling pathway activates CREB through PKA, p38 and MSK1 in NIH 3T3 cells. + Cell Signal + 2005 + Delghandi MP + Johannessen M + Moens U + + + 18184796 PubMed - Disrupted Homer scaffolds mediate abnormal mGluR5 function in a mouse model of fragile X syndrome. - Nat Neurosci - 2012 + Homer interactions are necessary for metabotropic glutamate receptor-induced long-term depression and translational activation. + J Neurosci + 2008 Ronesi JA - Collins KA - Hays SA - Tsai NP - Guo W - Birnbaum SG - Hu JH - Worley PF - Gibson JR Huber KM - - 23202739 + + 24966374 PubMed - Fragile X syndrome: causes, diagnosis, mechanisms, and therapeutics. - J Clin Invest - 2012 - Bagni C - Tassone F - Neri G - Hagerman R + NMDA Receptor-Dependent LTD Is Required for Consolidation But Not Acquisition of Fear Memory + The Journal of Neurosicence + 2014 + Xing Liu + Qin-Hua Gu + Kaizheng Duan + Zheng Li - - 20410124 + + 23576886 PubMed - Enhanced endocannabinoid signaling elevates neuronal excitability in fragile X syndrome. - J Neurosci - 2010 - Zhang L - Alger BE + AMPA receptor trafficking and the mechanisms underlying synaptic plasticity and cognitive aging. + Dialogues Clin Neurosci + 2013 + Henley JM + Wilkinson KA - - 10473536 + + 17644144 PubMed - The calcineurin-dynamin 1 complex as a calcium sensor for synaptic vesicle endocytosis. - J Biol Chem - 1999 - Lai MM - Hong JJ - Ruggiero AM - Burnett PE - Slepnev VI - De Camilli P - Snyder SH + Regulation of NMDA receptors by phosphorylation. + Neuropharmacology + 2007 + Chen BS + Roche KW - - 11837891 + + 20457613 PubMed - GABA and GABA receptors in the central nervous system and other organs. - Int Rev Cytol - 2002 - Watanabe M - Maemura K - Kanbara K - Tamayama T - Hayasaki H + Roles of fragile X mental retardation protein in dopaminergic stimulation-induced synapse-associated protein synthesis and subsequent alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-4-propionate (AMPA) receptor internalization. + J Biol Chem + 2010 + Wang H + Kim SS + Zhuo M 17084704 @@ -4394,51 +4411,6 @@ protein (CREB) at Ser133 Kuriyan J Bar-Sagi D - - 18215622 - PubMed - Molecular dissociation of the role of PSD-95 in regulating synaptic strength and LTD. - Neuron - 2008 - Xu W - Schlüter OM - Steiner P - Czervionke BL - Sabatini B - Malenka RC - - - 30686771 - PubMed - The translational regulator FMRP controls lipid and glucose metabolism in mice and humans. - Mol Metab - 2019 - Leboucher A - Pisani DF - Martinez-Gili L - Chilloux J - Bermudez-Martin P - Van Dijck A - Ganief T - Macek B - Becker JAJ - Le Merrer J - Kooy RF - Amri EZ - Khandjian EW - Dumas ME - Davidovic L - - - 20505079 - PubMed - Fragile X Mental Retardation Protein: Regulator of Specific mRNAs or Master Regulator of Global Translation? - Google Scholar - 2010 - Denise Cook - Scott A. Cameron - Emma V. Jones - 25781681 PubMed @@ -4451,41 +4423,88 @@ protein (CREB) at Ser133 Ladds G Rubio I - - 30364226 + + 23641197 PubMed - The Regulation of AMPA Receptor Endocytosis by Dynamic Protein-Protein Interactions. + FMRP: a triple threat to PSD-95. Front Cell Neurosci - 2018 - Hanley JG + 2013 + Westmark CJ - - 22405502 + + autism spectrum disorder + DOID:0060041 + Disease + + + 11237210 PubMed - Genetic manipulation of STEP reverses behavioral abnormalities in a fragile X syndrome mouse model. - Genes Brain Behav - 2012 - Goebel-Goody SM - Wilson-Wallis ED - Royston S - Tagliatela SM - Naegele JR - Lombroso PJ + Ras activation of the Raf kinase: tyrosine kinase recruitment of the MAP kinase cascade. + Recent Prog Horm Res + 2001 + Avruch J + Khokhlatchev A + Kyriakis JM + Luo Z + Tzivion G + Vavvas D + Zhang XF - - 18474609 + + 27239350 PubMed - S6K1 phosphorylates and regulates fragile X mental retardation protein (FMRP) with the neuronal protein synthesis-dependent mammalian target of rapamycin (mTOR) signaling cascade. - J Biol Chem - 2008 - Narayanan U - Nalavadi V - Nakamoto M - Thomas G - Ceman S - Bassell GJ + Synaptic Plasticity, a Prominent Contributor to the Anxiety in Fragile X Syndrome. + Neural Plast + 2016 + Yang T + Zhao H + Lu C + Li X + Xie Y + Fu H + Xu H + + + 15673435 + PubMed + Differential expression of two NMDA receptor interacting proteins, PSD-95 and SynGAP during mouse development. + Eur J Neurosci + 2005 + Porter K + Komiyama NH + Vitalis T + Kind PC + Grant SG + + + 15219735 + PubMed + The mGluR theory of fragile X mental retardation. + Trends Neurosci + 2004 + Bear MF + Huber KM Warren ST + + 20188650 + PubMed + Group 1 mGluR-dependent synaptic long-term depression: mechanisms and implications for circuitry and disease. + Neuron + 2010 + Lüscher C + Huber KM + + + disease pathway + PW:0000013 + Pathway Ontology + + + neuron + CL:0000540 + Cell Type + 17496911 PubMed @@ -4495,25 +4514,6 @@ protein (CREB) at Ser133 Z G Goldsmith D N Dhanasekaran - - 9783642216497 - ISBN - Modeling Fragile X Syndrome - Springer Books - 2011 - Robert B. Denman - - - 19436069 - PubMed - Ca2+/calmodulin-dependent protein kinase IV links group I metabotropic glutamate receptors to fragile X mental retardation protein in cingulate cortex. - J Biol Chem - 2009 - Wang H - Fukushima H - Kida S - Zhuo M - diff --git a/pathways/WP4549/WP4549.json b/pathways/WP4549/WP4549.json index 3be76d924..f9db625b5 100644 --- a/pathways/WP4549/WP4549.json +++ b/pathways/WP4549/WP4549.json @@ -31898,7 +31898,7 @@ "id": "publicationXrefa08", "source": "Philos Trans R Soc Lond B Biol Sci", "standardName": "Neurotrophin-regulated signalling pathways", - "textContent": "18", + "textContent": "19", "type": [ "PublicationXref", "PubMed:16939974" @@ -31919,7 +31919,7 @@ "id": "publicationXrefa19", "source": "Eur J Neurosci", "standardName": "Differential expression of two NMDA receptor interacting proteins, PSD-95 and SynGAP during mouse development.", - "textContent": "15", + "textContent": "16", "type": [ "PublicationXref", "PubMed:15673435" @@ -31937,7 +31937,7 @@ "id": "publicationXrefa1e", "source": "Korean J Physiol Pharmacol", "standardName": "Metabotropic glutamate receptor dependent long-term depression in the cortex.", - "textContent": "64", + "textContent": "63", "type": [ "PublicationXref", "PubMed:27847432" @@ -31957,7 +31957,7 @@ "id": "publicationXrefa20", "source": "Mol Biosyst", "standardName": "FMRP regulates miR196a-mediated repression of HOXB8 via interaction with the AGO2 MID domain.", - "textContent": "56", + "textContent": "54", "type": [ "PublicationXref", "PubMed:24727796" @@ -32003,7 +32003,7 @@ "id": "publicationXrefa46", "source": "Neural Plast", "standardName": "Impaired GABA Neural Circuits Are Critical for Fragile X Syndrome.", - "textContent": "73", + "textContent": "74", "type": [ "PublicationXref", "PubMed:30402088" @@ -32028,7 +32028,7 @@ "id": "publicationXrefa61", "source": "Cell", "standardName": "The postsynaptic density proteins Homer and Shank form a polymeric network structure.", - "textContent": "31", + "textContent": "30", "type": [ "PublicationXref", "PubMed:19345194" @@ -32046,7 +32046,7 @@ "id": "publicationXrefa67", "source": "Med Hypotheses", "standardName": "Activity-dependent alterations in the sensitivity to BDNF-TrkB signaling may promote excessive dendritic arborization and spinogenesis in fragile X syndrome in order to compensate for compromised postsynaptic activity.", - "textContent": "55", + "textContent": "56", "type": [ "PublicationXref", "PubMed:25113167" @@ -32063,7 +32063,7 @@ "id": "publicationXrefa79", "source": "Int J Biochem Cell Biol", "standardName": "Fyn, a Src family tyrosine kinase.", - "textContent": "2", + "textContent": "1", "type": [ "PublicationXref", "PubMed:9839441" @@ -32085,7 +32085,7 @@ "id": "publicationXrefa86", "source": "PLoS One", "standardName": "The cyclic AMP cascade is altered in the fragile X nervous system.", - "textContent": "22", + "textContent": "21", "type": [ "PublicationXref", "PubMed:17895972" @@ -32107,7 +32107,7 @@ "id": "publicationXrefa8a", "source": "Int J Physiol Pathophysiol Pharmacol", "standardName": "Regulation of GABAA receptors by fragile X mental retardation protein.", - "textContent": "50", + "textContent": "49", "type": [ "PublicationXref", "PubMed:24044036" @@ -32193,7 +32193,7 @@ "id": "publicationXrefafd", "source": "Neuron", "standardName": "Dynamic translational and proteasomal regulation of fragile X mental retardation protein controls mGluR-dependent long-term depression.", - "textContent": "19", + "textContent": "17", "type": [ "PublicationXref", "PubMed:16908410" @@ -32211,7 +32211,7 @@ "id": "publicationXrefb0a", "source": "J Neurosci Res", "standardName": "Fragile X mice: reduced long-term potentiation and N-Methyl-D-Aspartate receptor-mediated neurotransmission in dentate gyrus.", - "textContent": "40", + "textContent": "42", "type": [ "PublicationXref", "PubMed:21162125" @@ -32230,7 +32230,7 @@ "id": "publicationXrefb1b", "source": "Google Scholar", "standardName": "Fragile X Mental Retardation Protein: Regulator of Specific mRNAs or Master Regulator of Global Translation?", - "textContent": "39", + "textContent": "36", "type": [ "PublicationXref", "PubMed:20505079" @@ -32249,7 +32249,7 @@ "id": "publicationXrefb23", "source": "Genes Dev", "standardName": "A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins.", - "textContent": "6", + "textContent": "7", "type": [ "PublicationXref", "PubMed:12368261" @@ -32267,7 +32267,7 @@ "id": "publicationXrefb48", "source": "J Neurosci", "standardName": "Homer interactions are necessary for metabotropic glutamate receptor-induced long-term depression and translational activation.", - "textContent": "26", + "textContent": "28", "type": [ "PublicationXref", "PubMed:18184796" @@ -32288,7 +32288,7 @@ "id": "publicationXrefb4e", "source": "Front Mol Neurosci", "standardName": "Fragile-X Syndrome Is Associated With NMDA Receptor Hypofunction and Reduced Dendritic Complexity in Mature Dentate Granule Cells.", - "textContent": "76", + "textContent": "73", "type": [ "PublicationXref", "PubMed:30705620" @@ -32306,7 +32306,7 @@ "id": "publicationXrefb64", "source": "Dialogues Clin Neurosci", "standardName": "AMPA receptor trafficking and the mechanisms underlying synaptic plasticity and cognitive aging.", - "textContent": "49", + "textContent": "51", "type": [ "PublicationXref", "PubMed:23576886" @@ -32331,7 +32331,7 @@ "id": "publicationXrefb65", "source": "Neuron", "standardName": "Arc/Arg3.1 interacts with the endocytic machinery to regulate AMPA receptor trafficking.", - "textContent": "17", + "textContent": "18", "type": [ "PublicationXref", "PubMed:17088211" @@ -32376,7 +32376,7 @@ "id": "publicationXrefb85", "source": "J Biol Chem", "standardName": "S6K1 phosphorylates and regulates fragile X mental retardation protein (FMRP) with the neuronal protein synthesis-dependent mammalian target of rapamycin (mTOR) signaling cascade.", - "textContent": "28", + "textContent": "26", "type": [ "PublicationXref", "PubMed:18474609" @@ -32401,7 +32401,7 @@ "id": "publicationXrefb94", "source": "https://doi.org/10.1186/2040-2392-5-16", "standardName": "Divergent dysregulation of gene expression in murine models of fragile X syndrome and tuberous sclerosis", - "textContent": "53", + "textContent": "55", "type": [ "PublicationXref", "DOI:10.1186/2040-2392-5-16" @@ -32459,7 +32459,7 @@ "id": "publicationXrefbbc", "source": "J Clin Invest", "standardName": "Fragile X syndrome: causes, diagnosis, mechanisms, and therapeutics.", - "textContent": "47", + "textContent": "44", "type": [ "PublicationXref", "PubMed:23202739" @@ -32499,7 +32499,7 @@ "id": "publicationXrefbfd", "source": "Cold Spring Harb Perspect Biol", "standardName": "NMDA receptor-dependent long-term potentiation and long-term depression (LTP/LTD).", - "textContent": "45", + "textContent": "47", "type": [ "PublicationXref", "PubMed:22510460" @@ -32520,7 +32520,7 @@ "id": "publicationXrefc01", "source": "Google Scholar", "standardName": "Molecular Neurobiology of mTOR", - "textContent": "69", + "textContent": "71", "type": [ "PublicationXref", "PubMed:27889578" @@ -32539,7 +32539,7 @@ "id": "publicationXrefc0d", "source": "Curr Neuropharmacol", "standardName": "The role of ionotropic glutamate receptors in childhood neurodevelopmental disorders: autism spectrum disorders and fragile x syndrome.", - "textContent": "57", + "textContent": "53", "type": [ "PublicationXref", "PubMed:24533017" @@ -32562,7 +32562,7 @@ "id": "publicationXrefc27", "source": "PLoS One", "standardName": "New insights of altered lipid profile in Fragile X Syndrome.", - "textContent": "68", + "textContent": "69", "type": [ "PublicationXref", "PubMed:28334053" @@ -32598,7 +32598,7 @@ "id": "publicationXrefc3b", "source": "Cell Signal", "standardName": "The cAMP signalling pathway activates CREB through PKA, p38 and MSK1 in NIH 3T3 cells.", - "textContent": "16", + "textContent": "15", "type": [ "PublicationXref", "PubMed:16125054" @@ -32616,7 +32616,7 @@ "id": "publicationXrefc3d", "source": "Nature", "standardName": "Mechanisms of clathrin-mediated endocytosis", - "textContent": "74", + "textContent": "77", "type": [ "PublicationXref", "PubMed:29410531" @@ -32654,7 +32654,7 @@ "id": "publicationXrefc69", "source": "Annu Rev Genomics Hum Genet", "standardName": "Cognitive Dysfunctions in Intellectual Disabilities: The Contributions of the Ras-MAPK and PI3K-AKT-mTOR Pathways.", - "textContent": "72", + "textContent": "68", "type": [ "PublicationXref", "PubMed:28859574" @@ -32673,7 +32673,7 @@ "id": "publicationXrefc6a", "source": "Google Scholar", "standardName": "Molecular Mechanisms of Fragile X Syndrome: A Twenty-Year Perspective", - "textContent": "43", + "textContent": "45", "type": [ "PublicationXref", "PubMed:22017584" @@ -32690,7 +32690,7 @@ "id": "publicationXrefc99", "source": "Google Books", "standardName": "Intercellular Communication in the Nervous System", - "textContent": "34", + "textContent": "33", "type": [ "PublicationXref", "ISBN:9780123750723" @@ -32709,7 +32709,7 @@ "id": "publicationXrefcd6", "source": "Neurochem Res", "standardName": "From FMRP function to potential therapies for fragile X syndrome.", - "textContent": "58", + "textContent": "57", "type": [ "PublicationXref", "PubMed:24346713" @@ -32727,7 +32727,7 @@ "id": "publicationXrefce2", "source": "Biochem J", "standardName": "Molecular mechanisms of Dicer: endonuclease and enzymatic activity.", - "textContent": "70", + "textContent": "72", "type": [ "PublicationXref", "PubMed:28473628" @@ -32749,7 +32749,7 @@ "id": "publicationXrefcf2", "source": "Genes Brain Behav", "standardName": "Genetic manipulation of STEP reverses behavioral abnormalities in a fragile X syndrome mouse model.", - "textContent": "48", + "textContent": "43", "type": [ "PublicationXref", "PubMed:22405502" @@ -32766,7 +32766,7 @@ "id": "publicationXrefd04", "source": "http://edoc.unibas.ch/diss/DissB_6695; Institutional Repository of the University of Basel", "standardName": "Analysis of the Structure and Function of Protein Phosphatase 2A", - "textContent": "13", + "textContent": "12", "type": [ "PublicationXref", "DOI:10.5451/unibas-003209151" @@ -32805,7 +32805,7 @@ "id": "publicationXrefd25", "source": "The Journal of Neurosicence", "standardName": "NMDA Receptor-Dependent LTD Is Required for Consolidation But Not Acquisition of Fear Memory", - "textContent": "54", + "textContent": "58", "type": [ "PublicationXref", "PubMed:24966374" @@ -32825,7 +32825,7 @@ "id": "publicationXrefd35", "source": "J Biol Chem", "standardName": "Ca2+/calmodulin-dependent protein kinase IV links group I metabotropic glutamate receptors to fragile X mental retardation protein in cingulate cortex.", - "textContent": "32", + "textContent": "31", "type": [ "PublicationXref", "PubMed:19436069" @@ -32844,7 +32844,7 @@ "id": "publicationXrefd39", "source": "J Biol Chem", "standardName": "Roles of fragile X mental retardation protein in dopaminergic stimulation-induced synapse-associated protein synthesis and subsequent alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-4-propionate (AMPA) receptor internalization.", - "textContent": "36", + "textContent": "38", "type": [ "PublicationXref", "PubMed:20457613" @@ -32861,7 +32861,7 @@ "id": "publicationXrefd51", "source": "Springer Books", "standardName": "Modeling Fragile X Syndrome", - "textContent": "42", + "textContent": "40", "type": [ "PublicationXref", "ISBN:9783642216497" @@ -32879,7 +32879,7 @@ "id": "publicationXrefd7c", "source": "PLoS Biol", "standardName": "FMRP mediates mGluR5-dependent translation of amyloid precursor protein.", - "textContent": "23", + "textContent": "22", "type": [ "PublicationXref", "PubMed:17298186" @@ -32901,7 +32901,7 @@ "id": "publicationXrefd7d", "source": "Int J Physiol Pathophysiol Pharmacol", "standardName": "Regulation of GABAA receptors by fragile X mental retardation protein.", - "textContent": "51", + "textContent": "50", "type": [ "PublicationXref", "PubMed:24044036" @@ -32919,7 +32919,7 @@ "id": "publicationXrefd83", "source": "Dev Neurobiol", "standardName": "Postsynaptic BDNF-TrkB signaling in synapse maturation, plasticity, and disease.", - "textContent": "37", + "textContent": "35", "type": [ "PublicationXref", "PubMed:20186705" @@ -33021,7 +33021,7 @@ "id": "publicationXrefe42", "source": "Neuropharmacology", "standardName": "Regulation of NMDA receptors by phosphorylation.", - "textContent": "21", + "textContent": "23", "type": [ "PublicationXref", "PubMed:17644144" @@ -33057,7 +33057,7 @@ "id": "publicationXrefe4c", "source": "Biomed Res Int", "standardName": "ABC Transporter Subfamily D: Distinct Differences in Behavior between ABCD1-3 and ABCD4 in Subcellular Localization, Function, and Human Disease.", - "textContent": "63", + "textContent": "64", "type": [ "PublicationXref", "PubMed:27766264" @@ -33097,7 +33097,7 @@ "id": "publicationXrefe78", "source": "doi:10.1016/j.yapd.2009.08.008", "standardName": "Fragile X: A Family of Disorders", - "textContent": "33", + "textContent": "34", "type": [ "PublicationXref", "PubMed:19968948" @@ -33155,7 +33155,7 @@ "id": "publicationXrefe9d", "source": "Google Scholar", "standardName": "New insights into the regulatory function of CYFIP1 in the context of WAVE- and FMRP-containing complexes", - "textContent": "71", + "textContent": "70", "type": [ "PublicationXref", "PubMed:28183735" @@ -33176,7 +33176,7 @@ "id": "publicationXrefeb4", "source": "Genes Dev", "standardName": "4E-BP1, a repressor of mRNA translation, is phosphorylated and inactivated by the Akt(PKB) signaling pathway.", - "textContent": "1", + "textContent": "2", "type": [ "PublicationXref", "PubMed:9472019" @@ -33193,7 +33193,7 @@ "id": "publicationXrefece", "source": "Front Cell Neurosci", "standardName": "The Regulation of AMPA Receptor Endocytosis by Dynamic Protein-Protein Interactions.", - "textContent": "77", + "textContent": "76", "type": [ "PublicationXref", "PubMed:30364226" @@ -33263,7 +33263,7 @@ "id": "publicationXreff3d", "source": "Proc Natl Acad Sci U S A", "standardName": "Aberrant early-phase ERK inactivation impedes neuronal function in fragile X syndrome.", - "textContent": "25", + "textContent": "27", "type": [ "PublicationXref", "PubMed:18332424" @@ -33288,7 +33288,7 @@ "id": "publicationXreff78", "source": "Cell", "standardName": "The postsynaptic density proteins Homer and Shank form a polymericnetwork structure.", - "textContent": "30", + "textContent": "32", "type": [ "PublicationXref", "PubMed:19345194" @@ -33307,7 +33307,7 @@ "id": "publicationXreff83", "source": "Trends Neurosci", "standardName": "The mGluR theory of fragile X mental retardation.", - "textContent": "12", + "textContent": "13", "type": [ "PublicationXref", "PubMed:15219735" @@ -33326,7 +33326,7 @@ "id": "publicationXreff8b", "source": "Annu Rev Neurosci", "standardName": "The pathophysiology of fragile X (and what it teaches us about synapses).", - "textContent": "44", + "textContent": "48", "type": [ "PublicationXref", "PubMed:22483044" @@ -33347,7 +33347,7 @@ "id": "publicationXreff8c", "source": "Int Rev Cytol", "standardName": "GABA and GABA receptors in the central nervous system and other organs.", - "textContent": "7", + "textContent": "6", "type": [ "PublicationXref", "PubMed:11837891" @@ -33369,7 +33369,7 @@ "id": "publicationXreff91", "source": "Neuron", "standardName": "Molecular dissociation of the role of PSD-95 in regulating synaptic strength and LTD.", - "textContent": "27", + "textContent": "25", "type": [ "PublicationXref", "PubMed:18215622" @@ -33387,7 +33387,7 @@ "id": "publicationXreff94", "source": "Neuron", "standardName": "Group 1 mGluR-dependent synaptic long-term depression: mechanisms and implications for circuitry and disease.", - "textContent": "35", + "textContent": "39", "type": [ "PublicationXref", "PubMed:20188650" @@ -33405,7 +33405,7 @@ "id": "publicationXreffa0", "source": "J Neurosci", "standardName": "Enhanced endocannabinoid signaling elevates neuronal excitability in fragile X syndrome.", - "textContent": "38", + "textContent": "37", "type": [ "PublicationXref", "PubMed:20410124" @@ -34136,8 +34136,8 @@ "textContent": "Name: Fragile X syndrome\nLast Modified: 20240720055906\nOrganism: Homo sapiens", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0000013", - "http://identifiers.org/pw/PW:0001414" + "http://identifiers.org/pw/PW:0001414", + "http://identifiers.org/pw/PW:0000013" ], "verticalAlign": "top", "width": 5231.347826086948, diff --git a/pathways/WP4628/WP4628.gpml b/pathways/WP4628/WP4628.gpml index caca17d48..618770b9c 100644 --- a/pathways/WP4628/WP4628.gpml +++ b/pathways/WP4628/WP4628.gpml @@ -1142,6 +1142,16 @@ Referred article: [https://www.ncbi.nlm.nih.gov/pubmed/25009227 Shestov et al., Thummel CS Rutter J + + 0716730510 + ISBN + Biochemistry + https://www.ncbi.nlm.nih.gov/books/NBK22395/ + 2002 + Berg JM + Tymoczko JL + Stryer L + 25009227 PubMed @@ -1160,16 +1170,6 @@ Referred article: [https://www.ncbi.nlm.nih.gov/pubmed/25009227 Shestov et al., Albeck JG Locasale JW - - glycolysis/gluconeogenesis pathway - PW:0000025 - Pathway Ontology - - - cancer pathway - PW:0000605 - Pathway Ontology - 4729424 PubMed @@ -1181,21 +1181,21 @@ Referred article: [https://www.ncbi.nlm.nih.gov/pubmed/25009227 Shestov et al., Marco R Sols A - - 0716730510 - ISBN - Biochemistry - https://www.ncbi.nlm.nih.gov/books/NBK22395/ - 2002 - Berg JM - Tymoczko JL - Stryer L - + + glycolysis/gluconeogenesis pathway + PW:0000025 + Pathway Ontology + gluconeogenesis pathway PW:0000641 Pathway Ontology + + cancer pathway + PW:0000605 + Pathway Ontology + diff --git a/pathways/WP4628/WP4628.json b/pathways/WP4628/WP4628.json index 58f41757f..34601b3fc 100644 --- a/pathways/WP4628/WP4628.json +++ b/pathways/WP4628/WP4628.json @@ -11332,8 +11332,8 @@ "type": [ "Pathway", "http://identifiers.org/pw/PW:0000025", - "http://identifiers.org/pw/PW:0000605", - "http://identifiers.org/pw/PW:0000641" + "http://identifiers.org/pw/PW:0000641", + "http://identifiers.org/pw/PW:0000605" ], "verticalAlign": "top", "width": 1300, diff --git a/pathways/WP4707/WP4707.gpml b/pathways/WP4707/WP4707.gpml index cc738b678..0c10a5062 100644 --- a/pathways/WP4707/WP4707.gpml +++ b/pathways/WP4707/WP4707.gpml @@ -367,6 +367,11 @@ + + microRNA pathway + PW:0000808 + Pathway Ontology + acetylsalicylic acid drug pathway PW:0001613 @@ -387,11 +392,6 @@ Patullo L Kriegel AJ - - microRNA pathway - PW:0000808 - Pathway Ontology - diff --git a/pathways/WP4707/WP4707.json b/pathways/WP4707/WP4707.json index ee2c63351..bce5c8447 100644 --- a/pathways/WP4707/WP4707.json +++ b/pathways/WP4707/WP4707.json @@ -3443,8 +3443,8 @@ "textContent": "Name: Aspirin and miRNAs\nLast Modified: 20240720112358\nOrganism: Homo sapiens", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0001613", - "http://identifiers.org/pw/PW:0000808" + "http://identifiers.org/pw/PW:0000808", + "http://identifiers.org/pw/PW:0001613" ], "verticalAlign": "top", "width": 852.4001354096141, diff --git a/pathways/WP5038/WP5038-datanodes.tsv b/pathways/WP5038/WP5038-datanodes.tsv index fa06ba87e..dcc9ce716 100644 --- a/pathways/WP5038/WP5038-datanodes.tsv +++ b/pathways/WP5038/WP5038-datanodes.tsv @@ -1,59 +1,58 @@ -Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI -cGAMP Metabolite chebi:71580 "" wikidata:Q27139728 chebi:71580;chebi:71580 inchikey:RFCBNSCSPXMEBK-INFSMZHSSA-N -ROS Metabolite chebi:26523 "" wikidata:Q424361 chebi:26523;chebi:26523 -angiotensin-(1-9) Metabolite chebi:80128 "" wikidata:Q58310864 chebi:80128;chebi:80128 inchikey:LJXGOQOPNPFXFT-JWRYNVNRSA-N -angiotensin II Metabolite chebi:2719 "ang II accumulation" wikidata:Q412999 chebi:2719;chebi:2719 inchikey:CZGUSIXMZVURDU-JZXHSEFVSA-N -angiotensin I Metabolite chebi:2718 "" wikidata:Q539799 chebi:2718;chebi:2718 inchikey:ORWYRWWVDCYOMK-HBZPZAIKSA-N -AGT Metabolite chebi:2720 "" wikidata:Q267200 chebi:2720;chebi:2720 -angiotensin (1-7) Metabolite chebi:55438 "" wikidata:Q27074464 chebi:55438;chebi:55438 inchikey:PVHLMTREZMEJCG-GDTLVBQBSA-N -AGTR2 GeneProduct ensembl:ENSG00000180772 "" ensembl:ENSG00000180772 ncbigene:186 hgnc.symbol:AGTR2 uniprot:P50052 -MAS1 GeneProduct ensembl:ENSG00000206470 "" -NOX1 GeneProduct uniprot:Q9Y5S8 "" ensembl:ENSG00000007952 ncbigene:27035 hgnc.symbol:NOX1 uniprot:Q9Y5S8;uniprot:H0Y581;uniprot:Q5H9D4;uniprot:A6NGA6 -AGTR1 GeneProduct ensembl:ENSG00000144891 "" ensembl:ENSG00000144891 ncbigene:185 hgnc.symbol:AGTR1 uniprot:D3DNG8;uniprot:P30556;uniprot:A0A0A0MSE3;uniprot:Q53YY0 -cGAS GeneProduct uniprot:Q8N884 "" ensembl:ENSG00000164430 ncbigene:115004 hgnc.symbol:CGAS uniprot:Q8N884;uniprot:A0A7P0TBQ3 -ACAD9 GeneProduct ensembl:ENSG00000177646 "" ensembl:ENSG00000177646 ncbigene:28976 hgnc.symbol:ACAD9 uniprot:Q9H845;uniprot:A0A7P0T9N9;uniprot:A0A7P0TB68;uniprot:D6R9Z3;uniprot:D6RDK9;uniprot:D6RGK6;uniprot:A0A7P0TB58;uniprot:D6RCD8;uniprot:A0A7P0T7Z1;uniprot:Q9H9W4;uniprot:H0Y8Z9;uniprot:A0A7P0Z450;uniprot:A0A7P0T8U3;uniprot:D6RJA8;uniprot:A0A7P0T871 -NFKB1 GeneProduct ensembl:ENSG00000109320 "" ensembl:ENSG00000109320 ncbigene:4790 hgnc.symbol:NFKB1 uniprot:A0A494C157;uniprot:A0A494C1E9;uniprot:P19838;uniprot:D6RC45;uniprot:D6RH30 -DDX58 GeneProduct ensembl:ENSG00000107201 "" ensembl:ENSG00000107201 ncbigene:23586 hgnc.symbol:DDX58 uniprot:A0A7P0Z425;uniprot:B3KWW1;uniprot:O95786;uniprot:A0A7P0T9I8;uniprot:A0A7P0Z442;uniprot:A2A376 -IFIH1 GeneProduct hgnc.symbol:IFIH1 "" ensembl:ENSG00000115267 ncbigene:64135 hgnc.symbol:IFIH1 uniprot:A0A3B3IRK8;uniprot:Q9BYX4;uniprot:A0A7P0Z4A9 -NDUFAF1 GeneProduct ensembl:ENSG00000137806 "" ensembl:ENSG00000137806 ncbigene:51103 hgnc.symbol:NDUFAF1 uniprot:A0A7I2V4I7;uniprot:A0A024R9L0;uniprot:A0A7I2YQA4;uniprot:H0YL22;uniprot:Q9Y375;uniprot:H0YNB7;uniprot:H0YNN4 -BCS1L GeneProduct ensembl:ENSG00000074582 "" ensembl:ENSG00000074582 ncbigene:617 hgnc.symbol:BCS1L uniprot:C9JAS4;uniprot:H7BZF6;uniprot:C9J8G3;uniprot:Q9Y276;uniprot:A0A2R8Y7T3;uniprot:A0A024R445;uniprot:C9J4Q9;uniprot:H7C492;uniprot:C9J1S9 -ECSIT GeneProduct ensembl:ENSG00000130159 "" ensembl:ENSG00000130159 ncbigene:51295 hgnc.symbol:ECSIT uniprot:K7ESM8;uniprot:K7EIK2;uniprot:K7EM98;uniprot:K7EN32;uniprot:K7EPL5;uniprot:J3KTF5;uniprot:K7EJG5;uniprot:K7EJI1;uniprot:Q9BQ95 -NDUFB9 GeneProduct ensembl:ENSG00000147684 "" ensembl:ENSG00000147684 ncbigene:4715 hgnc.symbol:NDUFB9 uniprot:E7EWZ0;uniprot:A0A7I2V620;uniprot:E9PH64;uniprot:E9PF49;uniprot:A0A3B3IT57;uniprot:Q9Y6M9;uniprot:A0A7I2YQN0 -IKBKE GeneProduct ensembl:ENSG00000263528 "" ensembl:ENSG00000263528 ncbigene:9641 hgnc.symbol:IKBKE uniprot:A0A075B7C7;uniprot:A0A075B7B4;uniprot:A0A075B7D5;uniprot:Q14164 -CTSL GeneProduct ensembl:ENSG00000135047 "" ensembl:ENSG00000135047 ncbigene:1514 hgnc.symbol:CTSL uniprot:A0A7I2V2H7;uniprot:A0A7I2YQB5;uniprot:A0A7I2V5F7;uniprot:A0A024R276;uniprot:A0A7I2V601;uniprot:A0A7I2V5M3;uniprot:P07711;uniprot:A0A7I2YQA2;uniprot:Q5T8F0;uniprot:A0A7I2V484 -IRF3 GeneProduct ensembl:ENSG00000126456 "" ensembl:ENSG00000126456 ncbigene:3661 hgnc.symbol:IRF3 uniprot:M0R3C2;uniprot:M0R3H7;uniprot:M0R3E9;uniprot:M0QX56;uniprot:Q14653;uniprot:M0QYT9;uniprot:M0QZB7;uniprot:M0QZB8;uniprot:M0R0X9;uniprot:M0R0R8;uniprot:M0R007;uniprot:M0R205;uniprot:M0QYX3;uniprot:M0QXC8 -NFKB2 GeneProduct ensembl:ENSG00000077150 "" ensembl:ENSG00000077150 ncbigene:4791 hgnc.symbol:NFKB2 uniprot:Q00653 -TBK1 GeneProduct ensembl:ENSG00000183735 "" ensembl:ENSG00000183735 ncbigene:29110 hgnc.symbol:TBK1 uniprot:A0A494BZY3;uniprot:A0A494C148;uniprot:A0A494C045;uniprot:A0A7I2V3B7;uniprot:A0A494C167;uniprot:A0A7I2V4Y1;uniprot:A0A7I2V5W0;uniprot:F5H206;uniprot:A0A7I2V3Y6;uniprot:A0A7I2V5Y4;uniprot:A0A494C1I2;uniprot:A0A494C1M6;uniprot:A0A7I2V387;uniprot:A0A7I2V463;uniprot:A0A7I2V4S0;uniprot:A0A7I2V4W4;uniprot:A0A7I2YQM3;uniprot:A0A7I2V322;uniprot:A0A7I2V643;uniprot:A0A7I2YQG1;uniprot:A0A7I2V646;uniprot:A0A7I2V502;uniprot:A0A7I2YQG4;uniprot:A0A7I2V3S9;uniprot:A0A7I2V4M2;uniprot:F5H1A3;uniprot:A0A7I2V3E0;uniprot:F5GZI4;uniprot:A0A7I2V4M8;uniprot:A0A7I2V4C0;uniprot:A0A494C079;uniprot:A0A494C0R4;uniprot:A0A7I2V4Z2;uniprot:A0A7I2V5Z0;uniprot:A0A7I2V573;uniprot:A0A7I2V2N0;uniprot:A0A7I2V3P0;uniprot:A0A7I2V476;uniprot:A0A7I2V2V9;uniprot:A0A7I2V615;uniprot:A0A7I2V636;uniprot:A0A494C0A8;uniprot:A0A7I2V2N9;uniprot:Q9UHD2;uniprot:A0A494C0X2;uniprot:A0A7I2V2F4 -NLRX1 GeneProduct ensembl:ENSG00000160703 "" ensembl:ENSG00000160703 ncbigene:79671 hgnc.symbol:NLRX1 uniprot:C9J0R6;uniprot:C9JLK8;uniprot:C9JQE9;uniprot:Q86UT6 -IRF3 GeneProduct ensembl:ENSG00000126456 "" ensembl:ENSG00000126456 ncbigene:3661 hgnc.symbol:IRF3 uniprot:M0R3C2;uniprot:M0R3H7;uniprot:M0R3E9;uniprot:M0QX56;uniprot:Q14653;uniprot:M0QYT9;uniprot:M0QZB7;uniprot:M0QZB8;uniprot:M0R0X9;uniprot:M0R0R8;uniprot:M0R007;uniprot:M0R205;uniprot:M0QYX3;uniprot:M0QXC8 -TMPRSS2 GeneProduct ensembl:ENSG00000184012 "" ensembl:ENSG00000184012 ncbigene:7113;ncbigene:124905021 hgnc.symbol:TMPRSS2 uniprot:A0A7I2V474;uniprot:A0A7I2V650;uniprot:C9JKZ3;uniprot:O15393;uniprot:C9J5Y1;uniprot:A0A7I2V5F9;uniprot:A0A7I2V5N2;uniprot:A0A7I2V509;uniprot:A0A7I2V3D1;uniprot:A0A7I2YQ98;uniprot:C9JB05 -ACE2 GeneProduct uniprot:Q9BYF1 "" ensembl:ENSG00000130234 ncbigene:59272 hgnc.symbol:ACE2 uniprot:A0A7I2V3X6;uniprot:A0A7I2V5W5;uniprot:A0A7I2V2E9;uniprot:Q9BYF1;uniprot:A0A7I2V3N4;uniprot:A0A7I2V4H0 -IFN-I GeneProduct ncbigene:3438 "" -TMEM173 GeneProduct uniprot:Q86WV6 "STING1" ensembl:ENSG00000184584 ncbigene:340061 hgnc.symbol:STING1 uniprot:J3QTB1;uniprot:A0A494C0T1;uniprot:A0A494C0W5;uniprot:A0A494C1N5;uniprot:Q86WV6 -TLR3 GeneProduct ensembl:ENSG00000164342 "" ensembl:ENSG00000164342 ncbigene:7098 hgnc.symbol:TLR3 uniprot:D6RA51;uniprot:O15455 -TICAM1 GeneProduct ncbigene:148022 "TRIF" ensembl:ENSG00000127666 ncbigene:148022 hgnc.symbol:TICAM1 uniprot:Q8IUC6 -nsp13 GeneProduct wikidata:Q94648377 "" -orf6 GeneProduct uniprot:P0DTC6 "" -TRAF6 GeneProduct ensembl:ENSG00000175104 "" ensembl:ENSG00000175104 ncbigene:7189 hgnc.symbol:TRAF6 uniprot:Q9Y4K3 -TRAF3 GeneProduct ensembl:ENSG00000131323 "" ensembl:ENSG00000131323 ncbigene:7187 hgnc.symbol:TRAF3 uniprot:H0YL25;uniprot:H0YL26;uniprot:A6NHG8;uniprot:Q13114;uniprot:H0YMI8 -MAVS GeneProduct ensembl:ENSG00000088888 "" ensembl:ENSG00000088888 ncbigene:57506 hgnc.symbol:MAVS uniprot:Q7Z434 -PHB GeneProduct uniprot:P35232 "" ensembl:ENSG00000167085 ncbigene:5245 hgnc.symbol:PHB1 uniprot:P35232;uniprot:C9JW96;uniprot:A8K401;uniprot:E7ESE2;uniprot:E9PCW0;uniprot:C9JZ20 -PHB2 GeneProduct uniprot:Q99623 "" ensembl:ENSG00000215021 ncbigene:11331 hgnc.symbol:PHB2 uniprot:F5H2D2;uniprot:F5H3X6;uniprot:F5GWA7;uniprot:F5GY37;uniprot:J3KPX7;uniprot:A0A3G2KQ93;uniprot:F5H0C5;uniprot:Q99623;uniprot:U3KPZ5;uniprot:A0A7I2V5F0 -TLR7 GeneProduct ensembl:ENSG00000196664 "" ensembl:ENSG00000196664 ncbigene:51284 hgnc.symbol:TLR7 uniprot:B2R9N9;uniprot:Q9NYK1 -IRF7 GeneProduct ensembl:ENSG00000185507 "" ensembl:ENSG00000185507 ncbigene:3665 hgnc.symbol:IRF7 uniprot:A0A3B3ITQ5;uniprot:E9PIA7;uniprot:A0A024RCA2;uniprot:A0A3B3ISS4;uniprot:M9RSF4;uniprot:Q92985;uniprot:A0A3B3ISC0 -S2 Protein wikidata:Q106020384 "S2 subunit" -S1 Protein wikidata:Q106020256 "S1 subunit" -HSP90 Protein ensembl:ENSG00000080824.19 "" -orf9c Protein wikidata:Q104520877 "" -nsp7 Protein uniprot:P0DTD1 "" -ACE Protein uniprot:P12821 "" ensembl:ENSG00000159640 ncbigene:1636 hgnc.symbol:ACE uniprot:J3QSC7;uniprot:P12821;uniprot:J3KRH5;uniprot:J3KTH9;uniprot:J3QLR4;uniprot:J3KTB8;uniprot:J3KS28;uniprot:A0A0A0MSN4;uniprot:J3KSQ5 -Renin Protein uniprot:A0A1B0GUZ2 "" ensembl:ENSG00000143839 ncbigene:5972 hgnc.symbol:REN uniprot:P00797;uniprot:A0A1B0GUZ2 -Nucleoprotein N Protein uniprot:P0DTC9 "" -Spike Glycoprotein S Protein uniprot:P0DTC2 "" -Envelope Protein E Protein uniprot:P0DTC4 "" -Membrane Glycoprotein M Protein uniprot:P0DTC5 "" -nsp6 Protein ncbiprotein:YP_009725302 "" -orf9b Protein uniprot:P0DTD2 "promotes mitochondrial fusion" -TOMM70 Protein ensembl:ENSG00000154174 "" ensembl:ENSG00000154174 ncbigene:9868 hgnc.symbol:TOMM70 uniprot:O94826 -nsp2 Protein uniprot:P0DTD1 "impairs intra- cellular signaling and mitochondrial biogenesis" -PLpro Protein uniprot:P0DTD2 "" +Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI PubChem ChemSpider HMDB KEGG LipidMaps +cGAMP Metabolite chebi:71580 "" wikidata:Q27139728 chebi:71580 inchikey:RFCBNSCSPXMEBK-INFSMZHSSA-N pubchem.compound:11181459 chemspider:9356547 hmdb:HMDB0060465 +ROS Metabolite chebi:26523 "" wikidata:Q424361 chebi:26523 +angiotensin-(1-9) Metabolite chebi:80128 "" wikidata:Q58310864 chebi:80128 inchikey:LJXGOQOPNPFXFT-JWRYNVNRSA-N pubchem.compound:71745056 kegg.compound:C15851 +angiotensin II Metabolite chebi:2719 "ang II accumulation" wikidata:Q412999 chebi:2719 inchikey:CZGUSIXMZVURDU-JZXHSEFVSA-N pubchem.compound:172198 chemspider:150504 hmdb:HMDB0001035 kegg.compound:C02135 +angiotensin I Metabolite chebi:2718 "" wikidata:Q539799 chebi:2718 inchikey:ORWYRWWVDCYOMK-HBZPZAIKSA-N pubchem.compound:3081372 chemspider:23150106 hmdb:HMDB0061196 kegg.compound:C00873 +AGT Metabolite chebi:2720 "" wikidata:Q267200 chebi:2720 kegg.compound:C02246 +angiotensin (1-7) Metabolite chebi:55438 "" wikidata:Q27074464 chebi:55438 inchikey:PVHLMTREZMEJCG-GDTLVBQBSA-N pubchem.compound:123805 chemspider:110354 kegg.compound:C15850 +AGTR2 GeneProduct ensembl:ENSG00000180772 "" ensembl:ENSG00000180772 ncbigene:186 hgnc.symbol:AGTR2 uniprot:P50052 +MAS1 GeneProduct ensembl:ENSG00000206470 "" +NOX1 GeneProduct uniprot:Q9Y5S8 "" ensembl:ENSG00000007952 ncbigene:27035 hgnc.symbol:NOX1 uniprot:Q9Y5S8;uniprot:H0Y581;uniprot:Q5H9D4;uniprot:A6NGA6 +AGTR1 GeneProduct ensembl:ENSG00000144891 "" ensembl:ENSG00000144891 ncbigene:185 hgnc.symbol:AGTR1 uniprot:D3DNG8;uniprot:P30556;uniprot:A0A0A0MSE3;uniprot:Q53YY0 +cGAS GeneProduct uniprot:Q8N884 "" ensembl:ENSG00000164430 ncbigene:115004 hgnc.symbol:CGAS uniprot:Q8N884;uniprot:A0A7P0TBQ3 +ACAD9 GeneProduct ensembl:ENSG00000177646 "" ensembl:ENSG00000177646 ncbigene:28976 hgnc.symbol:ACAD9 uniprot:Q9H845;uniprot:A0A7P0T9N9;uniprot:A0A7P0TB68;uniprot:D6R9Z3;uniprot:D6RDK9;uniprot:D6RGK6;uniprot:A0A7P0TB58;uniprot:D6RCD8;uniprot:A0A7P0T7Z1;uniprot:Q9H9W4;uniprot:H0Y8Z9;uniprot:A0A7P0Z450;uniprot:A0A7P0T8U3;uniprot:D6RJA8;uniprot:A0A7P0T871 +NFKB1 GeneProduct ensembl:ENSG00000109320 "" ensembl:ENSG00000109320 ncbigene:4790 hgnc.symbol:NFKB1 uniprot:A0A494C157;uniprot:A0A494C1E9;uniprot:P19838;uniprot:D6RC45;uniprot:D6RH30 +DDX58 GeneProduct ensembl:ENSG00000107201 "" ensembl:ENSG00000107201 ncbigene:23586 hgnc.symbol:DDX58 uniprot:A0A7P0Z425;uniprot:B3KWW1;uniprot:O95786;uniprot:A0A7P0T9I8;uniprot:A0A7P0Z442;uniprot:A2A376 +IFIH1 GeneProduct hgnc.symbol:IFIH1 "" ensembl:ENSG00000115267 ncbigene:64135 hgnc.symbol:IFIH1 uniprot:A0A3B3IRK8;uniprot:Q9BYX4;uniprot:A0A7P0Z4A9 +NDUFAF1 GeneProduct ensembl:ENSG00000137806 "" ensembl:ENSG00000137806 ncbigene:51103 hgnc.symbol:NDUFAF1 uniprot:A0A7I2V4I7;uniprot:A0A024R9L0;uniprot:A0A7I2YQA4;uniprot:H0YL22;uniprot:Q9Y375;uniprot:H0YNB7;uniprot:H0YNN4 +BCS1L GeneProduct ensembl:ENSG00000074582 "" ensembl:ENSG00000074582 ncbigene:617 hgnc.symbol:BCS1L uniprot:C9JAS4;uniprot:H7BZF6;uniprot:C9J8G3;uniprot:Q9Y276;uniprot:A0A2R8Y7T3;uniprot:A0A024R445;uniprot:C9J4Q9;uniprot:H7C492;uniprot:C9J1S9 +ECSIT GeneProduct ensembl:ENSG00000130159 "" ensembl:ENSG00000130159 ncbigene:51295 hgnc.symbol:ECSIT uniprot:K7ESM8;uniprot:K7EIK2;uniprot:K7EM98;uniprot:K7EN32;uniprot:K7EPL5;uniprot:J3KTF5;uniprot:K7EJG5;uniprot:K7EJI1;uniprot:Q9BQ95 +NDUFB9 GeneProduct ensembl:ENSG00000147684 "" ensembl:ENSG00000147684 ncbigene:4715 hgnc.symbol:NDUFB9 uniprot:E7EWZ0;uniprot:A0A7I2V620;uniprot:E9PH64;uniprot:E9PF49;uniprot:A0A3B3IT57;uniprot:Q9Y6M9;uniprot:A0A7I2YQN0 +IKBKE GeneProduct ensembl:ENSG00000263528 "" ensembl:ENSG00000263528 ncbigene:9641 hgnc.symbol:IKBKE uniprot:A0A075B7C7;uniprot:A0A075B7B4;uniprot:A0A075B7D5;uniprot:Q14164 +CTSL GeneProduct ensembl:ENSG00000135047 "" ensembl:ENSG00000135047 ncbigene:1514 hgnc.symbol:CTSL uniprot:A0A7I2V2H7;uniprot:A0A7I2YQB5;uniprot:A0A7I2V5F7;uniprot:A0A024R276;uniprot:A0A7I2V601;uniprot:A0A7I2V5M3;uniprot:P07711;uniprot:A0A7I2YQA2;uniprot:Q5T8F0;uniprot:A0A7I2V484 +IRF3 GeneProduct ensembl:ENSG00000126456 "" ensembl:ENSG00000126456 ncbigene:3661 hgnc.symbol:IRF3 uniprot:M0R3C2;uniprot:M0R3H7;uniprot:M0R3E9;uniprot:M0QX56;uniprot:Q14653;uniprot:M0QYT9;uniprot:M0QZB7;uniprot:M0QZB8;uniprot:M0R0X9;uniprot:M0R0R8;uniprot:M0R007;uniprot:M0R205;uniprot:M0QYX3;uniprot:M0QXC8 +NFKB2 GeneProduct ensembl:ENSG00000077150 "" ensembl:ENSG00000077150 ncbigene:4791 hgnc.symbol:NFKB2 uniprot:Q00653 +TBK1 GeneProduct ensembl:ENSG00000183735 "" ensembl:ENSG00000183735 ncbigene:29110 hgnc.symbol:TBK1 uniprot:A0A494BZY3;uniprot:A0A494C148;uniprot:A0A494C045;uniprot:A0A7I2V3B7;uniprot:A0A494C167;uniprot:A0A7I2V4Y1;uniprot:A0A7I2V5W0;uniprot:F5H206;uniprot:A0A7I2V3Y6;uniprot:A0A7I2V5Y4;uniprot:A0A494C1I2;uniprot:A0A494C1M6;uniprot:A0A7I2V387;uniprot:A0A7I2V463;uniprot:A0A7I2V4S0;uniprot:A0A7I2V4W4;uniprot:A0A7I2YQM3;uniprot:A0A7I2V322;uniprot:A0A7I2V643;uniprot:A0A7I2YQG1;uniprot:A0A7I2V646;uniprot:A0A7I2V502;uniprot:A0A7I2YQG4;uniprot:A0A7I2V3S9;uniprot:A0A7I2V4M2;uniprot:F5H1A3;uniprot:A0A7I2V3E0;uniprot:F5GZI4;uniprot:A0A7I2V4M8;uniprot:A0A7I2V4C0;uniprot:A0A494C079;uniprot:A0A494C0R4;uniprot:A0A7I2V4Z2;uniprot:A0A7I2V5Z0;uniprot:A0A7I2V573;uniprot:A0A7I2V2N0;uniprot:A0A7I2V3P0;uniprot:A0A7I2V476;uniprot:A0A7I2V2V9;uniprot:A0A7I2V615;uniprot:A0A7I2V636;uniprot:A0A494C0A8;uniprot:A0A7I2V2N9;uniprot:Q9UHD2;uniprot:A0A494C0X2;uniprot:A0A7I2V2F4 +NLRX1 GeneProduct ensembl:ENSG00000160703 "" ensembl:ENSG00000160703 ncbigene:79671 hgnc.symbol:NLRX1 uniprot:C9J0R6;uniprot:C9JLK8;uniprot:C9JQE9;uniprot:Q86UT6 +TMPRSS2 GeneProduct ensembl:ENSG00000184012 "" ensembl:ENSG00000184012 ncbigene:7113;ncbigene:124905021 hgnc.symbol:TMPRSS2 uniprot:A0A7I2V474;uniprot:A0A7I2V650;uniprot:C9JKZ3;uniprot:O15393;uniprot:C9J5Y1;uniprot:A0A7I2V5F9;uniprot:A0A7I2V5N2;uniprot:A0A7I2V509;uniprot:A0A7I2V3D1;uniprot:A0A7I2YQ98;uniprot:C9JB05 +ACE2 GeneProduct uniprot:Q9BYF1 "" ensembl:ENSG00000130234 ncbigene:59272 hgnc.symbol:ACE2 uniprot:A0A7I2V3X6;uniprot:A0A7I2V5W5;uniprot:A0A7I2V2E9;uniprot:Q9BYF1;uniprot:A0A7I2V3N4;uniprot:A0A7I2V4H0 +IFN-I GeneProduct ncbigene:3438 "" +TMEM173 GeneProduct uniprot:Q86WV6 "STING1" ensembl:ENSG00000184584 ncbigene:340061 hgnc.symbol:STING1 uniprot:J3QTB1;uniprot:A0A494C0T1;uniprot:A0A494C0W5;uniprot:A0A494C1N5;uniprot:Q86WV6 +TLR3 GeneProduct ensembl:ENSG00000164342 "" ensembl:ENSG00000164342 ncbigene:7098 hgnc.symbol:TLR3 uniprot:D6RA51;uniprot:O15455 +TICAM1 GeneProduct ncbigene:148022 "TRIF" ensembl:ENSG00000127666 ncbigene:148022 hgnc.symbol:TICAM1 uniprot:Q8IUC6 +nsp13 GeneProduct wikidata:Q94648377 "" +orf6 GeneProduct uniprot:P0DTC6 "" +TRAF6 GeneProduct ensembl:ENSG00000175104 "" ensembl:ENSG00000175104 ncbigene:7189 hgnc.symbol:TRAF6 uniprot:Q9Y4K3 +TRAF3 GeneProduct ensembl:ENSG00000131323 "" ensembl:ENSG00000131323 ncbigene:7187 hgnc.symbol:TRAF3 uniprot:H0YL25;uniprot:H0YL26;uniprot:A6NHG8;uniprot:Q13114;uniprot:H0YMI8 +MAVS GeneProduct ensembl:ENSG00000088888 "" ensembl:ENSG00000088888 ncbigene:57506 hgnc.symbol:MAVS uniprot:Q7Z434 +PHB GeneProduct uniprot:P35232 "" ensembl:ENSG00000167085 ncbigene:5245 hgnc.symbol:PHB1 uniprot:P35232;uniprot:C9JW96;uniprot:A8K401;uniprot:E7ESE2;uniprot:E9PCW0;uniprot:C9JZ20 +PHB2 GeneProduct uniprot:Q99623 "" ensembl:ENSG00000215021 ncbigene:11331 hgnc.symbol:PHB2 uniprot:F5H2D2;uniprot:F5H3X6;uniprot:F5GWA7;uniprot:F5GY37;uniprot:J3KPX7;uniprot:A0A3G2KQ93;uniprot:F5H0C5;uniprot:Q99623;uniprot:U3KPZ5;uniprot:A0A7I2V5F0 +TLR7 GeneProduct ensembl:ENSG00000196664 "" ensembl:ENSG00000196664 ncbigene:51284 hgnc.symbol:TLR7 uniprot:B2R9N9;uniprot:Q9NYK1 +IRF7 GeneProduct ensembl:ENSG00000185507 "" ensembl:ENSG00000185507 ncbigene:3665 hgnc.symbol:IRF7 uniprot:A0A3B3ITQ5;uniprot:E9PIA7;uniprot:A0A024RCA2;uniprot:A0A3B3ISS4;uniprot:M9RSF4;uniprot:Q92985;uniprot:A0A3B3ISC0 +S2 Protein wikidata:Q106020384 "S2 subunit" +S1 Protein wikidata:Q106020256 "S1 subunit" +HSP90 Protein ensembl:ENSG00000080824.19 "" +orf9c Protein wikidata:Q104520877 "" +nsp7 Protein uniprot:P0DTD1 "" +ACE Protein uniprot:P12821 "" ensembl:ENSG00000159640 ncbigene:1636 hgnc.symbol:ACE uniprot:J3QSC7;uniprot:P12821;uniprot:J3KRH5;uniprot:J3KTH9;uniprot:J3QLR4;uniprot:J3KTB8;uniprot:J3KS28;uniprot:A0A0A0MSN4;uniprot:J3KSQ5 +Renin Protein uniprot:A0A1B0GUZ2 "" ensembl:ENSG00000143839 ncbigene:5972 hgnc.symbol:REN uniprot:P00797;uniprot:A0A1B0GUZ2 +Nucleoprotein N Protein uniprot:P0DTC9 "" +Spike Glycoprotein S Protein uniprot:P0DTC2 "" +Envelope Protein E Protein uniprot:P0DTC4 "" +Membrane Glycoprotein M Protein uniprot:P0DTC5 "" +nsp6 Protein ncbiprotein:YP_009725302 "" +orf9b Protein uniprot:P0DTD2 "promotes mitochondrial fusion" +TOMM70 Protein ensembl:ENSG00000154174 "" ensembl:ENSG00000154174 ncbigene:9868 hgnc.symbol:TOMM70 uniprot:O94826 +nsp2 Protein uniprot:P0DTD1 "impairs intra- cellular signaling and mitochondrial biogenesis" +PLpro Protein uniprot:P0DTD2 "" diff --git a/pathways/WP5038/WP5038.gpml b/pathways/WP5038/WP5038.gpml index e5766527e..9974e8556 100644 --- a/pathways/WP5038/WP5038.gpml +++ b/pathways/WP5038/WP5038.gpml @@ -1,5 +1,5 @@ - + SARS-CoV-2 mitochondrial immune response @@ -330,7 +330,6 @@ Induces viral uptake via ACE2 - Type your comment here a90 @@ -440,7 +439,6 @@ ACE2 binds to S1 subunit, to promote viral uptake and fusion at the cellular membrane - Type your comment here d3a @@ -628,7 +626,6 @@ S protein activated by CTSL/CTSB in the absence of ACE2 and/or TMPRSS2 in order to promote endocytosis - Type your comment here b42 @@ -645,7 +642,6 @@ TMPRSS2 activates the S protein by proteolytic cleavage of the site between S2 and S1 - Type your comment here f52 d3a @@ -1003,48 +999,6 @@ - - 33106987 - PubMed - Role of Oxidative Stress on SARS-CoV (SARS) and SARS-CoV-2 (COVID-19) Infection: A Review. - Protein J - 2020 - Suhail S - Zajac J - Fossum C - Lowater H - McCracken C - Severson N - Laatsch B - Narkiewicz-Jodko A - Johnson B - Liebau J - Bhattacharyya S - Hati S - - - 28956771 - PubMed - Inhibitory effect of parathion on the photosynthetic electron transport system in isolated spinach chloroplasts. - Bull Environ Contam Toxicol - 1975 - Schmoldt A - Benthe HF - Haberland G - Suzuki T - Uchiyama M - - - 31115493 - PubMed - Mitochondrial electron transport chain, ROS generation and uncoupling (Review). - Int J Mol Med - 2019 - Zhao RZ - Jiang S - Zhang L - Yu ZB - 33019591 PubMed @@ -1054,15 +1008,45 @@ Kreimendahl S Rassow J - - 32574107 + + 17451827 PubMed - Kawasaki-like diseases and thrombotic coagulopathy in COVID-19: delayed over-activation of the STING pathway? - Emerg Microbes Infect + SARS coronavirus and innate immunity. + Virus Res + 2008 + Frieman M + Heise M + Baric R + + + COVID-19 + DOID:0080600 + Disease + + + 32728199 + PubMed + SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. + Cell Mol Immunol 2020 - Berthelot JM - Drouet L - Lioté F + 32728199 + PubMed + SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. + Cell Mol Immunol + 2020 + Jiang HW + Zhang HN + Meng QF + Xie J + Li Y + Chen H + Zheng YX + Wang XN + Qi H + Zhang J + Wang PH + Han ZG + Tao SC 33015593 @@ -1101,11 +1085,257 @@ Koshiba T Millet GP + + 31115493 + PubMed + Mitochondrial electron transport chain, ROS generation and uncoupling (Review). + Int J Mol Med + 2019 + Zhao RZ + Jiang S + Zhang L + Yu ZB + + + severe acute respiratory syndrome + DOID:2945 + Disease + + + 32995797 + PubMed + SARS-CoV-2 induces double-stranded RNA-mediated innate immune responses in respiratory epithelial derived cells and cardiomyocytes. + bioRxiv + 2020 + Li Y + Renner DM + Comar CE + Whelan JN + Reyes HM + Cardenas-Diaz FL + Truitt R + Tan LH + Dong B + Alysandratos KD + Huang J + Palmer JN + Adappa ND + Kohanski MA + Kotton DN + Silverman RH + Yang W + Morrisey E + Cohen NA + Weiss SR + + + 21597473 + PubMed + Mitochondria in innate immune responses. + Nat Rev Immunol + 2011 + West AP + Shadel GS + Ghosh S + + + disease pathway + PW:0000013 + Pathway Ontology + immune response pathway PW:0000023 Pathway Ontology + + 32699849 + PubMed + Comparative multiplexed interactomics of SARS-CoV-2 and homologous coronavirus non-structural proteins identifies unique and shared host-cell dependencies. + bioRxiv + 2020 + Davies JP + Almasy KM + McDonald EF + Plate L + + + 32818486 + PubMed + Genes encoding ACE2, TMPRSS2 and related proteins mediating SARS-CoV-2 viral entry are upregulated with age in human cardiomyocytes. + J Mol Cell Cardiol + 2020 + Robinson EL + Alkass K + Bergmann O + Maguire JJ + Roderick HL + Davenport AP + + + 32839770 + PubMed + SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells. + bioRxiv + 2020 + Dominguez Andres A + Feng Y + Campos AR + Yin J + Yang CC + James B + Murad R + Kim H + Deshpande AJ + Gordon DE + Krogan N + Pippa R + Ronai ZA + + + 28956771 + PubMed + Inhibitory effect of parathion on the photosynthetic electron transport system in isolated spinach chloroplasts. + Bull Environ Contam Toxicol + 1975 + Schmoldt A + Benthe HF + Haberland G + Suzuki T + Uchiyama M + + + 32464637 + PubMed + + + + 32464637 + PubMed + The mechanistic overview of SARS-CoV-2 using angiotensin-converting enzyme 2 to enter the cell for replication: possible treatment options related to the renin-angiotensin system. + Eur Heart J Cardiovasc Pharmacother + 2020 + 32464637 + PubMed + The mechanistic overview of SARS-CoV-2 using angiotensin-converting enzyme 2 to enter the cell for replication: possible treatment options related to the renin-angiotensin system. + Eur Heart J Cardiovasc Pharmacother + 2020 + 32464637 + PubMed + The mechanistic overview of SARS-CoV-2 using angiotensin-converting enzyme 2 to enter the cell for replication: possible treatment options related to the renin-angiotensin system. + Offringa A + Montijn R + Singh S + Paul M + Pinto YM + Pinto-Sietsma SJ + + + 19692591 + PubMed + An N-terminal addressing sequence targets NLRX1 to the mitochondrial matrix. + J Cell Sci + 2009 + Arnoult D + Soares F + Tattoli I + Castanier C + Philpott DJ + Girardin SE + + + 21703540 + PubMed + NLRX1 protein attenuates inflammatory responses to infection by interfering with the RIG-I-MAVS and TRAF6-NF-κB signaling pathways. + Immunity + 2011 + Allen IC + Moore CB + Schneider M + Lei Y + Davis BK + Scull MA + Gris D + Roney KE + Zimmermann AG + Bowzard JB + Ranjan P + Monroe KM + Pickles RJ + Sambhara S + Ting JP + + + 33106987 + PubMed + Role of Oxidative Stress on SARS-CoV (SARS) and SARS-CoV-2 (COVID-19) Infection: A Review. + Protein J + 2020 + Suhail S + Zajac J + Fossum C + Lowater H + McCracken C + Severson N + Laatsch B + Narkiewicz-Jodko A + Johnson B + Liebau J + Bhattacharyya S + Hati S + + + 32574107 + PubMed + Kawasaki-like diseases and thrombotic coagulopathy in COVID-19: delayed over-activation of the STING pathway? + Emerg Microbes Infect + 2020 + Berthelot JM + Drouet L + Lioté F + + + 21187859 + PubMed + Crosstalk of reactive oxygen species and NF-κB signaling. + Cell Res + 2011 + Morgan MJ + Liu ZG + + + 32979938 + PubMed + Evasion of Type I Interferon by SARS-CoV-2. + Cell Rep + 2020 + Xia H + Cao Z + Xie X + Zhang X + Chen JY + Wang H + Menachery VD + Rajsbaum R + Shi PY + + + 33116300 + PubMed + + + + 33116300 + PubMed + Coronavirus biology and replication: implications for SARS-CoV-2. + Nat Rev Microbiol + 2020 + V'kovski P + Kratzel A + Steiner S + Stalder H + Thiel V + 32353859 PubMed @@ -1224,82 +1454,29 @@ Jura N von Zastrow M Verdin E - Ashworth A - Schwartz O - d'Enfert C - Mukherjee S - Jacobson M - Malik HS - Fujimori DG - Ideker T - Craik CS - Floor SN - Fraser JS - Gross JD - Sali A - Roth BL - Ruggero D - Taunton J - Kortemme T - Beltrao P - Vignuzzi M - García-Sastre A - Shokat KM - Shoichet BK - Krogan NJ - - - 32728199 - PubMed - SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. - Cell Mol Immunol - 2020 - 32728199 - PubMed - SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. - Cell Mol Immunol - 2020 - Jiang HW - Zhang HN - Meng QF - Xie J - Li Y - Chen H - Zheng YX - Wang XN - Qi H - Zhang J - Wang PH - Han ZG - Tao SC - - - disease pathway - PW:0000013 - Pathway Ontology - - - 21597473 - PubMed - Mitochondria in innate immune responses. - Nat Rev Immunol - 2011 - West AP - Shadel GS - Ghosh S - - - 32818486 - PubMed - Genes encoding ACE2, TMPRSS2 and related proteins mediating SARS-CoV-2 viral entry are upregulated with age in human cardiomyocytes. - J Mol Cell Cardiol - 2020 - Robinson EL - Alkass K - Bergmann O - Maguire JJ - Roderick HL - Davenport AP + Ashworth A + Schwartz O + d'Enfert C + Mukherjee S + Jacobson M + Malik HS + Fujimori DG + Ideker T + Craik CS + Floor SN + Fraser JS + Gross JD + Sali A + Roth BL + Ruggero D + Taunton J + Kortemme T + Beltrao P + Vignuzzi M + García-Sastre A + Shokat KM + Shoichet BK + Krogan NJ 33937724 @@ -1333,101 +1510,34 @@ Andrew C. Doxey Karen Mossman - - 32839770 - PubMed - SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells. - bioRxiv - 2020 - Dominguez Andres A - Feng Y - Campos AR - Yin J - Yang CC - James B - Murad R - Kim H - Deshpande AJ - Gordon DE - Krogan N - Pippa R - Ronai ZA - - - 32979938 - PubMed - Evasion of Type I Interferon by SARS-CoV-2. - Cell Rep - 2020 - Xia H - Cao Z - Xie X - Zhang X - Chen JY - Wang H - Menachery VD - Rajsbaum R - Shi PY - - - COVID-19 - DOID:0080600 - Disease - - - 33116300 - PubMed - - - - 33116300 - PubMed - Coronavirus biology and replication: implications for SARS-CoV-2. - Nat Rev Microbiol - 2020 - V'kovski P - Kratzel A - Steiner S - Stalder H - Thiel V - - - 32995797 - PubMed - SARS-CoV-2 induces double-stranded RNA-mediated innate immune responses in respiratory epithelial derived cells and cardiomyocytes. - bioRxiv - 2020 - Li Y - Renner DM - Comar CE - Whelan JN - Reyes HM - Cardenas-Diaz FL - Truitt R - Tan LH - Dong B - Alysandratos KD - Huang J - Palmer JN - Adappa ND - Kohanski MA - Kotton DN - Silverman RH - Yang W - Morrisey E - Cohen NA - Weiss SR - - - 32699849 + + 32726803 PubMed - Comparative multiplexed interactomics of SARS-CoV-2 and homologous coronavirus non-structural proteins identifies unique and shared host-cell dependencies. - bioRxiv + Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. + Nature 2020 - Davies JP - Almasy KM - McDonald EF - Plate L + Shin D + Mukherjee R + Grewe D + Bojkova D + Baek K + Bhattacharya A + Schulz L + Widera M + Mehdipour AR + Tascher G + Geurink PP + Wilhelm A + van der Heden van Noort GJ + Ovaa H + Müller S + Knobeloch KP + Rajalingam K + Schulman BA + Cinatl J + Hummer G + Ciesek S + Dikic I 23321557 @@ -1463,120 +1573,6 @@ Liming Cheng Jianmin Liu - - 21703540 - PubMed - NLRX1 protein attenuates inflammatory responses to infection by interfering with the RIG-I-MAVS and TRAF6-NF-κB signaling pathways. - Immunity - 2011 - Allen IC - Moore CB - Schneider M - Lei Y - Davis BK - Scull MA - Gris D - Roney KE - Zimmermann AG - Bowzard JB - Ranjan P - Monroe KM - Pickles RJ - Sambhara S - Ting JP - - - 21187859 - PubMed - Crosstalk of reactive oxygen species and NF-κB signaling. - Cell Res - 2011 - Morgan MJ - Liu ZG - - - 19692591 - PubMed - An N-terminal addressing sequence targets NLRX1 to the mitochondrial matrix. - J Cell Sci - 2009 - Arnoult D - Soares F - Tattoli I - Castanier C - Philpott DJ - Girardin SE - - - 17451827 - PubMed - SARS coronavirus and innate immunity. - Virus Res - 2008 - Frieman M - Heise M - Baric R - - - 32726803 - PubMed - Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. - Nature - 2020 - Shin D - Mukherjee R - Grewe D - Bojkova D - Baek K - Bhattacharya A - Schulz L - Widera M - Mehdipour AR - Tascher G - Geurink PP - Wilhelm A - van der Heden van Noort GJ - Ovaa H - Müller S - Knobeloch KP - Rajalingam K - Schulman BA - Cinatl J - Hummer G - Ciesek S - Dikic I - - - 32464637 - PubMed - - - - 32464637 - PubMed - The mechanistic overview of SARS-CoV-2 using angiotensin-converting enzyme 2 to enter the cell for replication: possible treatment options related to the renin-angiotensin system. - Eur Heart J Cardiovasc Pharmacother - 2020 - 32464637 - PubMed - The mechanistic overview of SARS-CoV-2 using angiotensin-converting enzyme 2 to enter the cell for replication: possible treatment options related to the renin-angiotensin system. - Eur Heart J Cardiovasc Pharmacother - 2020 - 32464637 - PubMed - The mechanistic overview of SARS-CoV-2 using angiotensin-converting enzyme 2 to enter the cell for replication: possible treatment options related to the renin-angiotensin system. - Offringa A - Montijn R - Singh S - Paul M - Pinto YM - Pinto-Sietsma SJ - - - severe acute respiratory syndrome - DOID:2945 - Disease - diff --git a/pathways/WP5038/WP5038.json b/pathways/WP5038/WP5038.json index 0dfedb5c5..b7a0369dc 100644 --- a/pathways/WP5038/WP5038.json +++ b/pathways/WP5038/WP5038.json @@ -443,8 +443,11 @@ "angiotensin II", "Wikidata:Q412999", "ChEBI:2719", - "ChEBI:2719", - "InChI:CZGUSIXMZVURDU-JZXHSEFVSA-N" + "InChI:CZGUSIXMZVURDU-JZXHSEFVSA-N", + "", + "", + "", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -703,8 +706,10 @@ "angiotensin (1-7)", "Wikidata:Q27074464", "ChEBI:55438", - "ChEBI:55438", - "InChI:PVHLMTREZMEJCG-GDTLVBQBSA-N" + "InChI:PVHLMTREZMEJCG-GDTLVBQBSA-N", + "", + "", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -2559,7 +2564,7 @@ "AGT", "Wikidata:Q267200", "ChEBI:2720", - "ChEBI:2720" + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -2626,8 +2631,10 @@ "cGAMP", "Wikidata:Q27139728", "ChEBI:71580", - "ChEBI:71580", - "InChI:RFCBNSCSPXMEBK-INFSMZHSSA-N" + "InChI:RFCBNSCSPXMEBK-INFSMZHSSA-N", + "", + "", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -6061,9 +6068,6 @@ "comments": [ { "content": "S protein activated by CTSL/CTSB in the absence of ACE2 and/or TMPRSS2 in order to promote endocytosis" - }, - { - "content": "Type your comment here" } ], "drawAs": "StraightLine", @@ -6151,8 +6155,11 @@ "angiotensin I", "Wikidata:Q539799", "ChEBI:2718", - "ChEBI:2718", - "InChI:ORWYRWWVDCYOMK-HBZPZAIKSA-N" + "InChI:ORWYRWWVDCYOMK-HBZPZAIKSA-N", + "", + "", + "", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -6364,9 +6371,6 @@ "comments": [ { "content": "ACE2 binds to S1 subunit, to promote viral uptake and fusion at the cellular membrane" - }, - { - "content": "Type your comment here" } ], "drawAs": "StraightLine", @@ -6763,7 +6767,6 @@ "CompactIdentifier:chebi:26523", "ROS", "Wikidata:Q424361", - "ChEBI:26523", "ChEBI:26523" ], "verticalAlign": "middle", @@ -7365,9 +7368,6 @@ "comments": [ { "content": "TMPRSS2 activates the S protein by proteolytic cleavage of the site between S2 and S1" - }, - { - "content": "Type your comment here" } ], "drawAs": "StraightLine", @@ -7557,8 +7557,9 @@ "angiotensin-(1-9)", "Wikidata:Q58310864", "ChEBI:80128", - "ChEBI:80128", - "InChI:LJXGOQOPNPFXFT-JWRYNVNRSA-N" + "InChI:LJXGOQOPNPFXFT-JWRYNVNRSA-N", + "", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -8583,9 +8584,6 @@ "comments": [ { "content": "Induces viral uptake via ACE2" - }, - { - "content": "Type your comment here" } ], "drawAs": "StraightLine", @@ -8718,7 +8716,7 @@ "id": "publicationXrefa90", "source": "Eur Heart J Cardiovasc Pharmacother", "standardName": "The mechanistic overview of SARS-CoV-2 using angiotensin-converting enzyme 2 to enter the cell for replication: possible treatment options related to the renin-angiotensin system.", - "textContent": "24", + "textContent": "16", "type": [ "PublicationXref", "PubMed:32464637" @@ -8754,7 +8752,7 @@ "id": "publicationXrefa96", "source": "bioRxiv", "standardName": "SARS-CoV-2 induces double-stranded RNA-mediated innate immune responses in respiratory epithelial derived cells and cardiomyocytes.", - "textContent": "20", + "textContent": "12", "type": [ "PublicationXref", "PubMed:32995797" @@ -8853,7 +8851,7 @@ "id": "publicationXrefb38", "source": "https://doi.org/10.1101/2020.06.18.158154", "standardName": "Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses", - "textContent": "16", + "textContent": "22", "type": [ "PublicationXref", "PubMed:33937724" @@ -8875,7 +8873,7 @@ "id": "publicationXrefb42", "source": "J Mol Cell Cardiol", "standardName": "Genes encoding ACE2, TMPRSS2 and related proteins mediating SARS-CoV-2 viral entry are upregulated with age in human cardiomyocytes.", - "textContent": "15", + "textContent": "14", "type": [ "PublicationXref", "PubMed:32818486" @@ -9016,7 +9014,7 @@ "id": "publicationXrefc3c", "source": "Nature", "standardName": "A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.", - "textContent": "13", + "textContent": "21", "type": [ "PublicationXref", "PubMed:32353859" @@ -9045,7 +9043,7 @@ "id": "publicationXrefd10", "source": "Cell Mol Immunol", "standardName": "SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70.", - "textContent": "14", + "textContent": "10", "type": [ "PublicationXref", "PubMed:32728199" @@ -9066,7 +9064,7 @@ "id": "publicationXrefd3a", "source": "Nat Rev Microbiol", "standardName": "Coronavirus biology and replication: implications for SARS-CoV-2.", - "textContent": "19", + "textContent": "20", "type": [ "PublicationXref", "PubMed:33116300" @@ -9128,7 +9126,7 @@ "id": "publicationXrefdd3", "source": "iScience", "standardName": "Mitochondria: In the Cross Fire of SARS-CoV-2 and Immunity.", - "textContent": "12", + "textContent": "11", "type": [ "PublicationXref", "PubMed:33015593" @@ -9146,7 +9144,7 @@ "id": "publicationXrefe1e", "source": "Int J Mol Sci", "standardName": "The Mitochondrial Outer Membrane Protein Tom70-Mediator in Protein Traffic, Membrane Contact Sites and Innate Immunity.", - "textContent": "10", + "textContent": "9", "type": [ "PublicationXref", "PubMed:33019591" @@ -9175,7 +9173,7 @@ "id": "publicationXrefe32", "source": "bioRxiv", "standardName": "SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells.", - "textContent": "17", + "textContent": "15", "type": [ "PublicationXref", "PubMed:32839770" @@ -9203,7 +9201,7 @@ "id": "publicationXrefe6e", "source": "Protein J", "standardName": "Role of Oxidative Stress on SARS-CoV (SARS) and SARS-CoV-2 (COVID-19) Infection: A Review.", - "textContent": "9", + "textContent": "17", "type": [ "PublicationXref", "PubMed:33106987" @@ -9223,7 +9221,7 @@ "id": "publicationXrefee2", "source": "bioRxiv", "standardName": "Comparative multiplexed interactomics of SARS-CoV-2 and homologous coronavirus non-structural proteins identifies unique and shared host-cell dependencies.", - "textContent": "21", + "textContent": "13", "type": [ "PublicationXref", "PubMed:32699849" @@ -9248,7 +9246,7 @@ "id": "publicationXrefefa", "source": "Cell Rep", "standardName": "Evasion of Type I Interferon by SARS-CoV-2.", - "textContent": "18", + "textContent": "19", "type": [ "PublicationXref", "PubMed:32979938" @@ -9330,7 +9328,7 @@ "id": "publicationXreff52", "source": "https://doi.org/10.1101/2020.02.08.926006", "standardName": "The insert sequence in SARS-CoV-2 enhances spike protein cleavage by TMPRSS", - "textContent": "22", + "textContent": "24", "type": [ "PublicationXref", "DOI:10.1101/2020.02.08.926006" @@ -9349,7 +9347,7 @@ "id": "publicationXreffc7", "source": "Emerg Microbes Infect", "standardName": "Kawasaki-like diseases and thrombotic coagulopathy in COVID-19: delayed over-activation of the STING pathway?", - "textContent": "11", + "textContent": "18", "type": [ "PublicationXref", "PubMed:32574107" @@ -9660,7 +9658,7 @@ "id57f20ac8", "b0078" ], - "dataSourceVersion": "WP5038_r129286", + "dataSourceVersion": "WP5038_r134348", "displayName": "Mitochondrial immune response to SARS-CoV-2", "drawAs": "rect", "fill": "white", @@ -9670,7 +9668,7 @@ "height": 2027.1428571428573, "id": "WP5038", "kaavioType": "Group", - "lastModified": "20240319184519", + "lastModified": "20240720152510", "name": "Mitochondrial immune response to SARS-CoV-2", "organism": "Homo sapiens", "padding": 5, @@ -9679,11 +9677,11 @@ "stroke": "black", "strokeWidth": 0, "textAlign": "left", - "textContent": "Name: Mitochondrial immune response to SARS-CoV-2\nLast Modified: 20240319184519\nOrganism: Homo sapiens", + "textContent": "Name: Mitochondrial immune response to SARS-CoV-2\nLast Modified: 20240720152510\nOrganism: Homo sapiens", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0000023", - "http://identifiers.org/pw/PW:0000013" + "http://identifiers.org/pw/PW:0000013", + "http://identifiers.org/pw/PW:0000023" ], "verticalAlign": "top", "width": 2258.571428571429, diff --git a/pathways/WP5038/WP5038.png b/pathways/WP5038/WP5038.png index 17fbaec1f..4eed71aed 100644 Binary files a/pathways/WP5038/WP5038.png and b/pathways/WP5038/WP5038.png differ diff --git a/pathways/WP5038/WP5038.svg b/pathways/WP5038/WP5038.svg index 258e8d443..8523ed3d7 100644 --- a/pathways/WP5038/WP5038.svg +++ b/pathways/WP5038/WP5038.svg @@ -508,7 +508,7 @@ - + @@ -1468,7 +1468,7 @@ Name: Mitochondrial immune response to SARS-CoV-2 - Last Modified: 20240319184519 + Last Modified: 20240720152510 Organism: Homo sapiens diff --git a/pathways/WP5474/WP5474.gpml b/pathways/WP5474/WP5474.gpml index 5217b87f5..f667dcdff 100644 --- a/pathways/WP5474/WP5474.gpml +++ b/pathways/WP5474/WP5474.gpml @@ -705,14 +705,115 @@ + + 18054315 + PubMed + FoxO3 controls autophagy in skeletal muscle in vivo. + Cell Metab + 2007 + Mammucari C + Milan G + Romanello V + Masiero E + Rudolf R + Del Piccolo P + Burden SJ + Di Lisi R + Sandri C + Zhao J + Goldberg AL + Schiaffino S + Sandri M + + + 15479644 + PubMed + IKKbeta/NF-kappaB activation causes severe muscle wasting in mice. + Cell + 2004 + Cai D + Frantz JD + Tawa NE Jr + Melendez PA + Oh BC + Lidov HG + Hasselgren PO + Frontera WR + Lee J + Glass DJ + Shoelson SE + + + 34950660 + PubMed + Weight Loss in Cancer Patients Correlates With p38β MAPK Activation in Skeletal Muscle. + Front Cell Dev Biol + 2021 + Zhang G + Anderson LJ + Gao S + Sin TK + Zhang Z + Wu H + Jafri SH + Graf SA + Wu PC + Dash A + Garcia JM + Li YP + + + 24002653 + PubMed + Smad3 induces atrogin-1, inhibits mTOR and protein synthesis, and promotes muscle atrophy in vivo. + Mol Endocrinol + 2013 + Goodman CA + McNally RM + Hoffmann FM + Hornberger TA + + + 32933049 + PubMed + MuRF1/TRIM63, Master Regulator of Muscle Mass. + Int J Mol Sci + 2020 + Peris-Moreno D + Taillandier D + Polge C + + + 24550918 + PubMed + Role of the TWEAK-Fn14-cIAP1-NF-κB Signaling Axis in the Regulation of Myogenesis and Muscle Homeostasis. + Front Immunol + 2014 + Enwere EK + Lacasse EC + Adam NJ + Korneluk RG + - signaling pathway - PW:0000003 - Pathway Ontology + cancer + DOID:162 + Disease + + 23517348 + PubMed + Mechanisms regulating skeletal muscle growth and atrophy. + FEBS J + 2013 + Schiaffino S + Dyar KA + Ciciliot S + Blaauw B + Sandri M + - disease pathway - PW:0000013 + signaling pathway + PW:0000003 Pathway Ontology @@ -727,16 +828,18 @@ Navon A Goldberg AL - - cancer - DOID:162 - Disease - - - muscle cell - CL:0000187 - Cell Type - + + 35626710 + PubMed + Interleukin-1 and Nuclear Factor Kappa B Signaling Promote Breast Cancer Progression and Treatment Resistance. + Cells + 2022 + Diep S + Maddukuri M + Yamauchi S + Geshow G + Delk NA + 35841281 PubMed @@ -751,28 +854,14 @@ Pfeffer LM Donner DB - - 23517348 - PubMed - Mechanisms regulating skeletal muscle growth and atrophy. - FEBS J - 2013 - Schiaffino S - Dyar KA - Ciciliot S - Blaauw B - Sandri M - - - 24002653 + + 17374508 PubMed - Smad3 induces atrogin-1, inhibits mTOR and protein synthesis, and promotes muscle atrophy in vivo. - Mol Endocrinol - 2013 - Goodman CA - McNally RM - Hoffmann FM - Hornberger TA + The myostatin gene: physiology and pharmacological relevance. + Curr Opin Pharmacol + 2007 + Joulia-Ekaza D + Cabello G 15109499 @@ -791,20 +880,33 @@ Lecker SH Goldberg AL - - 17374508 - PubMed - The myostatin gene: physiology and pharmacological relevance. - Curr Opin Pharmacol - 2007 - Joulia-Ekaza D - Cabello G - - cell of skeletal muscle - CL:0000188 + muscle cell + CL:0000187 Cell Type + + 18061509 + PubMed + How the Smads regulate transcription. + Int J Biochem Cell Biol + 2008 + Ross S + Hill CS + + + 28264935 + PubMed + STAT3 promotes IFNγ/TNFα-induced muscle wasting in an NF-κB-dependent and IL-6-independent manner. + EMBO Mol Med + 2017 + Ma JF + Sanchez BJ + Hall DT + Tremblay AK + Di Marco S + Gallouzi IE + 30228872 PubMed @@ -816,15 +918,16 @@ Russell A Lamon S - - 11003979 - PubMed - NF-kappaB mediates the protein loss induced by TNF-alpha in differentiated skeletal muscle myotubes. - Am J Physiol Regul Integr Comp Physiol - 2000 - Li YP - Reid MB - + + disease pathway + PW:0000013 + Pathway Ontology + + + cell of skeletal muscle + CL:0000188 + Cell Type + PMC3423125 PubMed @@ -832,122 +935,19 @@ Am J Physiol Endocrinol Metab. 2012 - - 28264935 - PubMed - STAT3 promotes IFNγ/TNFα-induced muscle wasting in an NF-κB-dependent and IL-6-independent manner. - EMBO Mol Med - 2017 - Ma JF - Sanchez BJ - Hall DT - Tremblay AK - Di Marco S - Gallouzi IE - cancer pathway PW:0000605 Pathway Ontology - - 32933049 - PubMed - MuRF1/TRIM63, Master Regulator of Muscle Mass. - Int J Mol Sci - 2020 - Peris-Moreno D - Taillandier D - Polge C - - - 24550918 - PubMed - Role of the TWEAK-Fn14-cIAP1-NF-κB Signaling Axis in the Regulation of Myogenesis and Muscle Homeostasis. - Front Immunol - 2014 - Enwere EK - Lacasse EC - Adam NJ - Korneluk RG - - - 18061509 - PubMed - How the Smads regulate transcription. - Int J Biochem Cell Biol - 2008 - Ross S - Hill CS - - - 18054315 - PubMed - FoxO3 controls autophagy in skeletal muscle in vivo. - Cell Metab - 2007 - Mammucari C - Milan G - Romanello V - Masiero E - Rudolf R - Del Piccolo P - Burden SJ - Di Lisi R - Sandri C - Zhao J - Goldberg AL - Schiaffino S - Sandri M - - - 34950660 + + 11003979 PubMed - Weight Loss in Cancer Patients Correlates With p38β MAPK Activation in Skeletal Muscle. - Front Cell Dev Biol - 2021 - Zhang G - Anderson LJ - Gao S - Sin TK - Zhang Z - Wu H - Jafri SH - Graf SA - Wu PC - Dash A - Garcia JM + NF-kappaB mediates the protein loss induced by TNF-alpha in differentiated skeletal muscle myotubes. + Am J Physiol Regul Integr Comp Physiol + 2000 Li YP - - - 35626710 - PubMed - Interleukin-1 and Nuclear Factor Kappa B Signaling Promote Breast Cancer Progression and Treatment Resistance. - Cells - 2022 - Diep S - Maddukuri M - Yamauchi S - Geshow G - Delk NA - - - 15479644 - PubMed - IKKbeta/NF-kappaB activation causes severe muscle wasting in mice. - Cell - 2004 - Cai D - Frantz JD - Tawa NE Jr - Melendez PA - Oh BC - Lidov HG - Hasselgren PO - Frontera WR - Lee J - Glass DJ - Shoelson SE + Reid MB diff --git a/pathways/WP5474/WP5474.json b/pathways/WP5474/WP5474.json index edd7e816c..969a7dcaa 100644 --- a/pathways/WP5474/WP5474.json +++ b/pathways/WP5474/WP5474.json @@ -6546,7 +6546,7 @@ "id": "publicationXrefa9f", "source": "Cell", "standardName": "IKKbeta/NF-kappaB activation causes severe muscle wasting in mice.", - "textContent": "4", + "textContent": "3", "type": [ "PublicationXref", "PubMed:15479644" @@ -6592,7 +6592,7 @@ "id": "publicationXrefb52", "source": "Curr Opin Pharmacol", "standardName": "The myostatin gene: physiology and pharmacological relevance.", - "textContent": "5", + "textContent": "6", "type": [ "PublicationXref", "PubMed:17374508" @@ -6621,7 +6621,7 @@ "id": "publicationXrefbb4", "source": "Cell Metab", "standardName": "FoxO3 controls autophagy in skeletal muscle in vivo.", - "textContent": "6", + "textContent": "5", "type": [ "PublicationXref", "PubMed:18054315" @@ -6734,7 +6734,7 @@ "id": "publicationXrefcd4", "source": "Cells", "standardName": "Interleukin-1 and Nuclear Factor Kappa B Signaling Promote Breast Cancer Progression and Treatment Resistance.", - "textContent": "17", + "textContent": "16", "type": [ "PublicationXref", "PubMed:35626710" @@ -6755,7 +6755,7 @@ "id": "publicationXrefd89", "source": "FEBS J", "standardName": "Mechanisms regulating skeletal muscle growth and atrophy.", - "textContent": "9", + "textContent": "10", "type": [ "PublicationXref", "PubMed:23517348" @@ -6778,7 +6778,7 @@ "id": "publicationXrefd8c", "source": "J Cell Mol Med", "standardName": "STAT3 regulates inflammatory cytokine production downstream of TNFR1 by inducing expression of TNFAIP3/A20.", - "textContent": "16", + "textContent": "17", "type": [ "PublicationXref", "PubMed:35841281" @@ -6804,7 +6804,7 @@ "id": "publicationXrefdab", "source": "Cell", "standardName": "Foxo transcription factors inducethe atrophy-related ubiquitin ligase atrogin-1 and cause skeletal muscle atrophy.", - "textContent": "3", + "textContent": "4", "type": [ "PublicationXref", "PubMed:15109499" @@ -6863,7 +6863,7 @@ "id": "publicationXrefea1", "source": "Mol Endocrinol", "standardName": "Smad3 induces atrogin-1, inhibits mTOR and protein synthesis, and promotes muscle atrophy in vivo.", - "textContent": "10", + "textContent": "9", "type": [ "PublicationXref", "PubMed:24002653" diff --git a/pathways/WP5485/WP5485.gpml b/pathways/WP5485/WP5485.gpml index aa5f1e72a..8b09b227b 100644 --- a/pathways/WP5485/WP5485.gpml +++ b/pathways/WP5485/WP5485.gpml @@ -684,64 +684,45 @@ the humoral route also involves the local release of pro-inflammatory cytokines - - 37163427 - PubMed - Complications of COVID-19 on the Central Nervous System: Mechanisms and Potential Treatment for Easing Long COVID. - Aging Dis - 2023 - Wei ZD - Liang K - Shetty AK - - - 34086044 + + 34770863 PubMed - Expression of the SARS-CoV-2 Receptor ACE2 in Human Retina and Diabetes-Implications for Retinopathy. - Invest Ophthalmol Vis Sci + A Review of Human Coronaviruses' Receptors: The Host-Cell Targets for the Crown Bearing Viruses. + Molecules 2021 - Zhou L - Xu Z - Guerra J - Rosenberg AZ - Fenaroli P - Eberhart CG - Duh EJ - - - 36570463 - PubMed - Investigating neurological symptoms of infectious diseases like COVID-19 leading to a deeper understanding of neurodegenerative disorders such as Parkinson's disease. - Front Neurol - 2022 - Zhang J + Nassar A + Ibrahim IM + Amin FG + Magdy M + Elgharib AM + Azzam EB + Nasser F + Yousry K + Shamkh IM + Mahdy SM + Elfiky AA - - 36899952 + + 38037103 PubMed - Pathogenesis Underlying Neurological Manifestations of Long COVID Syndrome and Potential Therapeutics. - Cells + Reactive oxygen species (ROS) scavenging biomaterials for anti-inflammatory diseases: from mechanism to therapy. + J Hematol Oncol 2023 - Leng A - Shah M - Ahmad SA - Premraj L - Wildi K - Li Bassi G - Pardo CA - Choi A - Cho SM + Liu J + Han X + Zhang T + Tian K + Li Z + Luo F - - 37894116 + + 35955708 PubMed - Long COVID-19 Pathophysiology: What Do We Know So Far? - Microorganisms - 2023 - Tziolos NR - Ioannou P - Baliou S - Kofteridis DP + The Role of Neuro-Immune Interaction in Chronic Pain Conditions; Functional Somatic Syndrome, Neurogenic Inflammation, and Peripheral Neuropathy. + Int J Mol Sci + 2022 + Meade E + Garvey M 38590789 @@ -765,40 +746,6 @@ the humoral route also involves the local release of pro-inflammatory cytokines Pallanti S Makris N - - 37327802 - PubMed - Tachykinins and the potential causal factors for post-COVID-19 condition. - Lancet Microbe - 2023 - Janket SJ - Fraser DD - Baird AE - Tamimi F - Sohaei D - Conte HA - Prassas I - Diamandis EP - - - 35955708 - PubMed - The Role of Neuro-Immune Interaction in Chronic Pain Conditions; Functional Somatic Syndrome, Neurogenic Inflammation, and Peripheral Neuropathy. - Int J Mol Sci - 2022 - Meade E - Garvey M - - - COVID-19 - DOID:0080600 - Disease - - - neutrophil - CL:0000775 - Cell Type - 37388279 PubMed @@ -809,14 +756,11 @@ the humoral route also involves the local release of pro-inflammatory cytokines Wilson DR Agrawal DK - - 34884216 - PubMed - Dysautonomia and Implications for Anosmia in Long COVID-19 Disease. - J Clin Med - 2021 - Vallée A - + + COVID-19 + DOID:0080600 + Disease + 37064029 PubMed @@ -827,47 +771,52 @@ the humoral route also involves the local release of pro-inflammatory cytokines Low RJ Akrami A - - 34770863 + + 36947108. PubMed - A Review of Human Coronaviruses' Receptors: The Host-Cell Targets for the Crown Bearing Viruses. - Molecules + Pathogenic mechanisms of post-acute sequelae of SARS-CoV-2 infection (PASC). + Elife + 2023 + Sherif ZA + Gomez CR + Connors TJ + Henrich TJ + Reeves WB + + + 34248921 + PubMed + Long COVID or Post-acute Sequelae of COVID-19 (PASC): An Overview of Biological Factors That May Contribute to Persistent Symptoms. + Front Microbiol 2021 - Nassar A - Ibrahim IM - Amin FG - Magdy M - Elgharib AM - Azzam EB - Nasser F - Yousry K - Shamkh IM - Mahdy SM - Elfiky AA + Proal AD + VanElzakker MB - - 38037103 + + 38131885 PubMed - Reactive oxygen species (ROS) scavenging biomaterials for anti-inflammatory diseases: from mechanism to therapy. - J Hematol Oncol + Persisting Shadows: Unraveling the Impact of Long COVID-19 on Respiratory, Cardiovascular, and Nervous Systems. + Infect Dis Rep 2023 - Liu J - Han X - Zhang T - Tian K - Li Z - Luo F + Sideratou CM + Papaneophytou C + + + 36899952 + PubMed + Pathogenesis Underlying Neurological Manifestations of Long COVID Syndrome and Potential Therapeutics. + Cells + 2023 + Leng A + Shah M + Ahmad SA + Premraj L + Wildi K + Li Bassi G + Pardo CA + Choi A + Cho SM - - macrophage - CL:0000235 - Cell Type - - - monocyte - CL:0000576 - Cell Type - 36189286 PubMed @@ -881,43 +830,74 @@ the humoral route also involves the local release of pro-inflammatory cytokines Zhan S Liu J - - 38337760 + + 34086044 PubMed - The Multisystem Impact of Long COVID: A Comprehensive Review. - Diagnostics (Basel) - 2024 - Negrut N - Menegas G - Kampioti S - Bourelou M - Kopanyi F - Hassan FD - Asowed A - Taleouine FZ - Ferician A - Marian P + Expression of the SARS-CoV-2 Receptor ACE2 in Human Retina and Diabetes-Implications for Retinopathy. + Invest Ophthalmol Vis Sci + 2021 + Zhou L + Xu Z + Guerra J + Rosenberg AZ + Fenaroli P + Eberhart CG + Duh EJ - - 36947108 + + 37327802 PubMed - Pathogenic mechanisms of post-acute sequelae of SARS-CoV-2 infection (PASC). - Elife + Tachykinins and the potential causal factors for post-COVID-19 condition. + Lancet Microbe 2023 - Sherif ZA - Gomez CR - Connors TJ - Henrich TJ - Reeves WB + Janket SJ + Fraser DD + Baird AE + Tamimi F + Sohaei D + Conte HA + Prassas I + Diamandis EP - - 34248921 + + neutrophil + CL:0000775 + Cell Type + + + macrophage + CL:0000235 + Cell Type + + + 34884216 PubMed - Long COVID or Post-acute Sequelae of COVID-19 (PASC): An Overview of Biological Factors That May Contribute to Persistent Symptoms. - Front Microbiol + Dysautonomia and Implications for Anosmia in Long COVID-19 Disease. + J Clin Med 2021 - Proal AD - VanElzakker MB + Vallée A + + + 35629421 + PubMed + Prevention and Treatment of Life-Threatening COVID-19 May Be Possible with Oxygen Treatment. + Life (Basel) + 2022 + Ylikoski J + Lehtimäki J + Pääkkönen R + Mäkitie A + + + 37894116 + PubMed + Long COVID-19 Pathophysiology: What Do We Know So Far? + Microorganisms + 2023 + Tziolos NR + Ioannou P + Baliou S + Kofteridis DP 38037103. @@ -932,17 +912,16 @@ the humoral route also involves the local release of pro-inflammatory cytokines Li Z Luo F - - 35629421 - PubMed - Prevention and Treatment of Life-Threatening COVID-19 May Be Possible with Oxygen Treatment. - Life (Basel) - 2022 - Ylikoski J - Lehtimäki J - Pääkkönen R - Mäkitie A - + + signaling pathway + PW:0000003 + Pathway Ontology + + + natural killer cell + CL:0000623 + Cell Type + 36580747 PubMed @@ -958,19 +937,49 @@ the humoral route also involves the local release of pro-inflammatory cytokines Abou-Kheir W Lawand N + + 38337760 + PubMed + The Multisystem Impact of Long COVID: A Comprehensive Review. + Diagnostics (Basel) + 2024 + Negrut N + Menegas G + Kampioti S + Bourelou M + Kopanyi F + Hassan FD + Asowed A + Taleouine FZ + Ferician A + Marian P + + + 37163427 + PubMed + Complications of COVID-19 on the Central Nervous System: Mechanisms and Potential Treatment for Easing Long COVID. + Aging Dis + 2023 + Wei ZD + Liang K + Shetty AK + - natural killer cell - CL:0000623 + monocyte + CL:0000576 Cell Type - - 38131885 + + 36947108 PubMed - Persisting Shadows: Unraveling the Impact of Long COVID-19 on Respiratory, Cardiovascular, and Nervous Systems. - Infect Dis Rep + Pathogenic mechanisms of post-acute sequelae of SARS-CoV-2 infection (PASC). + Elife 2023 - Sideratou CM - Papaneophytou C + Sherif ZA + Gomez CR + Connors TJ + Henrich TJ + Reeves WB 34400495 @@ -983,23 +992,14 @@ the humoral route also involves the local release of pro-inflammatory cytokines Komaroff AL Snyder SH - - 36947108. + + 36570463 PubMed - Pathogenic mechanisms of post-acute sequelae of SARS-CoV-2 infection (PASC). - Elife - 2023 - Sherif ZA - Gomez CR - Connors TJ - Henrich TJ - Reeves WB + Investigating neurological symptoms of infectious diseases like COVID-19 leading to a deeper understanding of neurodegenerative disorders such as Parkinson's disease. + Front Neurol + 2022 + Zhang J - - signaling pathway - PW:0000003 - Pathway Ontology - diff --git a/pathways/WP5485/WP5485.json b/pathways/WP5485/WP5485.json index 5e0da0665..ac8999456 100644 --- a/pathways/WP5485/WP5485.json +++ b/pathways/WP5485/WP5485.json @@ -6263,7 +6263,7 @@ "id": "publicationXrefa5b", "source": "Int J Mol Sci", "standardName": "The Role of Neuro-Immune Interaction in Chronic Pain Conditions; Functional Somatic Syndrome, Neurogenic Inflammation, and Peripheral Neuropathy.", - "textContent": "7", + "textContent": "6", "type": [ "PublicationXref", "PubMed:35955708" @@ -6284,7 +6284,7 @@ "id": "publicationXrefa8a", "source": "Elife", "standardName": "Pathogenic mechanisms of post-acute sequelae of SARS-CoV-2 infection (PASC).", - "textContent": "17", + "textContent": "21", "type": [ "PublicationXref", "PubMed:36947108" @@ -6305,7 +6305,7 @@ "id": "publicationXrefaba", "source": "Elife", "standardName": "Pathogenic mechanisms of post-acute sequelae of SARS-CoV-2 infection (PASC).", - "textContent": "21", + "textContent": "13", "type": [ "PublicationXref", "PubMed:36947108." @@ -6356,7 +6356,7 @@ "id": "publicationXrefb9f", "source": "Life (Basel)", "standardName": "Prevention and Treatment of Life-Threatening COVID-19 May Be Possible with Oxygen Treatment.", - "textContent": "9", + "textContent": "8", "type": [ "PublicationXref", "PubMed:35629421" @@ -6374,7 +6374,7 @@ "id": "publicationXrefbca", "source": "Front Microbiol", "standardName": "Long COVID or Post-acute Sequelae of COVID-19 (PASC): An Overview of Biological Factors That May Contribute to Persistent Symptoms.", - "textContent": "4", + "textContent": "2", "type": [ "PublicationXref", "PubMed:34248921" @@ -6413,7 +6413,7 @@ "id": "publicationXrefc56", "source": "Front Neurol", "standardName": "Investigating neurological symptoms of infectious diseases like COVID-19 leading to a deeper understanding of neurodegenerative disorders such as Parkinson's disease.", - "textContent": "6", + "textContent": "9", "type": [ "PublicationXref", "PubMed:36570463" @@ -6458,7 +6458,7 @@ "id": "publicationXrefc9a", "source": "Arch Microbiol Immunol", "standardName": "Long COVID: Complications, Underlying Mechanisms, and Treatment Strategies.", - "textContent": "14", + "textContent": "11", "type": [ "PublicationXref", "PubMed:37388279" @@ -6503,7 +6503,7 @@ "id": "publicationXrefcc3", "source": "Cells", "standardName": "Pathogenesis Underlying Neurological Manifestations of Long COVID Syndrome and Potential Therapeutics.", - "textContent": "11", + "textContent": "15", "type": [ "PublicationXref", "PubMed:36899952" @@ -6521,7 +6521,7 @@ "id": "publicationXrefcd9", "source": "Infect Dis Rep", "standardName": "Persisting Shadows: Unraveling the Impact of Long COVID-19 on Respiratory, Cardiovascular, and Nervous Systems.", - "textContent": "20", + "textContent": "14", "type": [ "PublicationXref", "PubMed:38131885" @@ -6543,7 +6543,7 @@ "id": "publicationXrefd18", "source": "Front Immunol", "standardName": "Bioinformatics and systems biology approach to identify the pathogenetic link of Long COVID and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome.", - "textContent": "8", + "textContent": "7", "type": [ "PublicationXref", "PubMed:36189286" @@ -6563,7 +6563,7 @@ "id": "publicationXrefdf0", "source": "Microorganisms", "standardName": "Long COVID-19 Pathophysiology: What Do We Know So Far?", - "textContent": "12", + "textContent": "17", "type": [ "PublicationXref", "PubMed:37894116" @@ -6590,7 +6590,7 @@ "id": "publicationXrefe17", "source": "Molecules", "standardName": "A Review of Human Coronaviruses' Receptors: The Host-Cell Targets for the Crown Bearing Viruses.", - "textContent": "3", + "textContent": "1", "type": [ "PublicationXref", "PubMed:34770863" @@ -6612,7 +6612,7 @@ "id": "publicationXrefe7a", "source": "J Hematol Oncol", "standardName": "Reactive oxygen species (ROS) scavenging biomaterials for anti-inflammatory diseases: from mechanism to therapy.", - "textContent": "16", + "textContent": "10", "type": [ "PublicationXref", "PubMed:38037103" @@ -6635,7 +6635,7 @@ "id": "publicationXrefe7b", "source": "Invest Ophthalmol Vis Sci", "standardName": "Expression of the SARS-CoV-2 Receptor ACE2 in Human Retina and Diabetes-Implications for Retinopathy.", - "textContent": "1", + "textContent": "3", "type": [ "PublicationXref", "PubMed:34086044" @@ -6654,7 +6654,7 @@ "id": "publicationXrefee7", "source": "Front Med (Lausanne)", "standardName": "A review of cytokine-based pathophysiology of Long COVID symptoms.", - "textContent": "15", + "textContent": "12", "type": [ "PublicationXref", "PubMed:37064029" @@ -6678,7 +6678,7 @@ "id": "publicationXreff10", "source": "Lancet Microbe", "standardName": "Tachykinins and the potential causal factors for post-COVID-19 condition.", - "textContent": "13", + "textContent": "16", "type": [ "PublicationXref", "PubMed:37327802" @@ -6695,7 +6695,7 @@ "id": "publicationXreff74", "source": "J Clin Med", "standardName": "Dysautonomia and Implications for Anosmia in Long COVID-19 Disease.", - "textContent": "2", + "textContent": "4", "type": [ "PublicationXref", "PubMed:34884216" @@ -6714,7 +6714,7 @@ "id": "publicationXreffb3", "source": "Aging Dis", "standardName": "Complications of COVID-19 on the Central Nervous System: Mechanisms and Potential Treatment for Easing Long COVID.", - "textContent": "10", + "textContent": "20", "type": [ "PublicationXref", "PubMed:37163427"