GeneFEAST: the pivotal, gene-centric step in functional enrichment analysis interpretation.

IF 5.4 Bioinformatics (Oxford, England) Pub Date : 2025-03-04 DOI:10.1093/bioinformatics/btaf100

Avigail Taylor, Valentine M Macaulay, Matthieu J Miossec, Anand K Maurya, Francesca M Buffa

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Abstract

Summary: GeneFEAST, implemented in Python, is a gene-centric functional enrichment analysis summarization and visualization tool that can be applied to large functional enrichment analysis (FEA) results arising from upstream FEA pipelines. It produces a systematic, navigable HTML report, making it easy to identify sets of genes putatively driving multiple enrichments and to explore gene-level quantitative data first used to identify input genes. Further, GeneFEAST can juxtapose FEA results from multiple studies, making it possible to highlight patterns of gene expression amongst genes that are differentially expressed in at least one of multiple conditions, and which give rise to shared enrichments under those conditions. Thus, GeneFEAST offers a novel, effective way to address the complexities of linking up many overlapping FEA results to their underlying genes and data, advancing gene-centric hypotheses, and providing pivotal information for downstream validation experiments.

Availability and implementation: GeneFEAST GitHub repository: https://github.com/avigailtaylor/GeneFEAST; Zenodo record: 10.5281/zenodo.14753734; Python Package Index: https://pypi.org/project/genefeast; Docker container: ghcr.io/avigailtaylor/genefeast.

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GeneFEAST：功能富集分析解释中关键的、以基因为中心的一步。

GeneFEAST是一个以基因为中心的功能富集分析总结和可视化工具，可以应用于上游FEA管道产生的大型功能富集分析（FEA）结果。它生成了一个系统的、可导航的HTML报告，使识别假定驱动多重富集的基因集和探索最初用于识别输入基因的基因水平定量数据变得容易。此外，GeneFEAST可以将多个研究的FEA结果并列，从而有可能突出在多种条件下至少一种差异表达的基因之间的基因表达模式，并在这些条件下产生共享富集。因此，GeneFEAST提供了一种新颖有效的方法来解决将许多重叠的FEA结果与其潜在基因和数据联系起来的复杂性，推进以基因为中心的假设，并为下游验证实验提供关键信息。可用性和实现：GeneFEAST GitHub存储库：https://github.com/avigailtaylor/GeneFEAST；Zenodo记录：10.5281/ Zenodo .14753734；Python包索引：https://pypi.org/project/genefeast；Docker容器：ghcr.io/avigailtaylor/genefeast。补充信息：补充信息可在生物信息学网站在线获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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