Baltoumas, F. | bioRxiv Science

bioRxiv2023

Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources

Functional enrichment is the process of identifying implicated functional terms from a given input list of genes or proteins. In this article, we present Flame (v2.0), a web tool which offers a combinatorial approach through merging and visualizing results from widely-used functional enrichment applications while also allowing various flexible input options. In this version, Flame utilizes the aGOtool, g:Profiler, WebGestalt and Enrichr pipelines and presents their outputs separately or in combination following a visual analytics approach. For intuitive representations and easier interpretation, it uses interactive plots such as parameterizable networks, heatmaps, barcharts and scatter plots. Users can also: (i) handle multiple protein/gene lists and analyze union and intersection sets simultaneously through interactive UpSet plots, (ii) automatically extract genes and proteins from free text through text-mining and Named Entity Recognition (NER) techniques, (iii) upload single nucleotide polymorphisms (SNPs) and extract their relative genes or (iv) analyze multiple lists of differentially-expressed proteins/genes after selecting them interactively from a parameterizable volcano plot. Compared to the previous version of 197 supported organisms, Flame (v2.0) currently allows enrichment for 14,436 organisms.

bioinformatics↗

bioRxiv2021

FLAME: a web tool for functional and literature enrichment analysis of multiple gene lists

Functional enrichment is a widely used method for interpreting experimental results by identifying classes of proteins/genes associated with certain biological functions, pathways, diseases or phenotypes. Despite the variety of existing tools, most of them can process a single list per time, thus making a more combinatorial analysis more complicated and prone to errors. In this article, we present FLAME, a web tool for combining multiple lists prior to enrichment analysis. Users can upload several lists of preference and use interactive UpSet plots, as an alternative to Venn diagrams, to handle unions or intersections among the given input files. Functional and literature enrichment along with gene conversions are offered by g:Profiler and aGOtool applications for 197 organisms. In its current version, FLAME can analyze genes/proteins for related articles, Gene Ontologies, pathways, annotations, regulatory motifs, domains, diseases, phenotypes while it can also generate protein-protein interactions derived from STRING. We have herein validated FLAME by interrogating gene expression data associated with the sensitivity of the distal part of the large intestine to experimental colitis-propelled colon cancer. The FLAME application comes with an interactive user-friendly interface which allows easy list manipulation and exploration, while results can be visualized as interactive and parameterizable heatmaps, barcharts, Manhattan plots, networks and tables. AvailabilityFLAME application: http://flame.pavlopouloslab.info Codehttps://github.com/PavlopoulosLab/FLAME

bioinformatics↗