Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari (Athens), 16672, Greece.
Department of Mathematics, University of Thessaly, Lamia, 35100, Greece.
Bioinformatics. 2023 Aug 1;39(8). doi: 10.1093/bioinformatics/btad490.
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 analyse 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) analyse 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.
Web Application: http://flame.pavlopouloslab.info. Code: https://github.com/PavlopoulosLab/Flame. Docker: https://hub.docker.com/r/pavlopouloslab/flame.
功能富集是从给定的基因或蛋白质输入列表中识别相关功能术语的过程。在本文中，我们介绍了 Flame（v2.0），这是一个网络工具，它提供了一种组合方法，通过合并和可视化来自广泛使用的功能富集应用程序的结果，同时还允许各种灵活的输入选项。在这个版本中，Flame 利用了 aGOtool、g:Profiler、WebGestalt 和 Enrichr 管道，并以可视化分析的方式分别或组合呈现它们的输出。为了直观的表示和更方便的解释，它使用了交互式的图，如可参数化的网络、热图、柱状图和散点图。用户还可以：（i）处理多个蛋白质/基因列表，并通过交互式 Upset 图同时分析并集和交集集，（ii）通过文本挖掘和命名实体识别（NER）技术自动从自由文本中提取基因和蛋白质，（iii）上传单核苷酸多态性（SNP）并提取其相对基因，或（iv）在从可参数化火山图中交互选择后，分析多个差异表达蛋白质/基因列表。与以前的 197 个支持的生物体版本相比，Flame（v2.0）现在允许对 14436 个生物体进行富集。
