Enhancing TFEA.ChIP with ENCODE regulatory maps for generalizable transcription factor enrichment.

ABSTRACT: Identifying transcription factors (TFs) responsible for gene expression changes remain a central challenge in functional genomics. TFEA.ChIP is a ChIP-seq-based TF enrichment analysis tool that addresses this by linking TF binding profiles to differentially expressed genes through experimentally supported cis-regulatory element (CRE)-gene associations. Unlike motif- or heuristic-based approaches, TFEA.ChIP adopts a biologically grounded strategy by intersecting TF binding data from ReMap2022 with regulatory maps from ENCODE's rE2G and CREdb. To overcome the high context-specificity of rE2G associations, we developed filtering strategies based on confidence scores and recurrence across biosamples. Benchmarking on 342 curated gene sets from the Molecular Signatures Database C2 CGP collection

SUBMITTER: Berrouayel Y 

PROVIDER: S-EPMC12796816 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature