Flame

Visualization and interpretation of functional and literature enrichment analysis results from multiple sets

With Flame one can:

• Upload multiple gene/protein lists, SNPs, free text or gene expression results (Volcano plot)
• Combine lists by calculating their unions and intersections with the help of UpSet plots
• Perform functional enrichment analysis on any of the combined lists for more than 14,000 organisms, using four tools (aGOtool, gProfiler, WebGestalt, enrichR)
• Combine and compare enrichment results from multiple runs
• Perform literature enrichment analysis on any of the combined lists, using aGOtool
• Generate protein-protein interaction networks via STRING
• Visualize results with the use of networks, heatmaps, bar charts, scatter plots and searchable tables
• Perform network analysis at the gene-function, function-function and gene-gene association levels
• Visualize networks in interactive, multi-layered views with Arena3Dweb
• Combine data sources and apply interactive filters on the generated plots
• Perform cross-database and cross-species id conversions
• Utilize our API to connect Flame with external applications

Flame is written in R/Shiny and JavaScript and is available at http://flame.pavlopouloslab.info

Installation

• Download and install the Flame image from Docker Hub: https://hub.docker.com/r/pavlopouloslab/flame

• Otherwise, download this GitHub repo and run Flame via RStudio. R (https://www.r-project.org/) and RStudio (https://rstudio.com/) must be installed. Make sure the following R libraries are also installed: shinyjs, shinyalert, bsplus, upsetjs, stringr, httr, httpuv, curl, jsonlite, gprofiler2, WebGestaltR, shinydashboard, shinyWidgets, DT, tidyr, enrichR, plotly, igraph, visNetwork. To start the program, double click on the Flame.Rproj file. This opens the RStudio process. Then, open the server.R file in RStudio and in the Run App options choose "Run External" and then click Run App.

Cite

1. Karatzas, E., Baltoumas, F.A., Aplakidou, E., Kontou, P.I., Stathopoulos, P., Stefanis, L., Bagos, P.G. and Pavlopoulos, G.A. (2023) Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources Bioinformatics, Volume 39, Issue 8, August 2023, btad490 https://doi.org/10.1093/bioinformatics/btad490
2. Thanati, F., Karatzas, E., Baltoumas, F.A., Stravopodis, D.J., Eliopoulos, A.G. and Pavlopoulos, G.A. (2021) FLAME: a web tool for functional and literature enrichment analysis of multiple gene lists. Biology, 10(7), p.665, doi: 10.3390/biology10070665 https://www.mdpi.com/2079-7737/10/7/665