Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources
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Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.21.529389v1?rss=1

Authors: Karatzas, E., Baltoumas, F., Aplakidou, E., Kontou, P., Stathopoulos, P., Stefanis, L., Bagos, P., Pavlopoulos, G. A.

Abstract: 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.

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