GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data.

ABSTRACT: Extraction of meaningful biological insight from gene expression profiling often focuses on the identification of statistically enriched terms or pathways. These methods typically use gene sets as input data, and subsequently return overrepresented terms along with associated statistics describing their enrichment. This approach does not cater to analyses focused on a single gene-of-interest, particularly when the gene lacks prior functional characterization. To address this, we formulated GeneCOCOA, a method which utilizes context-specific gene co-expression and curated functional gene sets, but focuses on a user-supplied gene-of-interest (GOI). The co-expression between the GOI and subsets of genes from functional groups (e.g. pathways, GO terms) is derived using linear regression, and r

SUBMITTER: Zehr S 

PROVIDER: S-EPMC11964461 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature