Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression.

ABSTRACT:

Motivation

Gene set enrichment methods are a common tool to improve the interpretability of gene lists as obtained, for example, from differential gene expression analyses. They are based on computing whether dysregulated genes are located in certain biological pathways more often than expected by chance. Gene set enrichment tools rely on pre-existing pathway databases such as KEGG, Reactome, or the Gene Ontology. These databases are increasing in size and in the number of redundancies between pathways, which complicates the statistical enrichment computation.

Results

We address this problem and develop a novel gene set enrichment method, called pareg, which is based on a regularized generalized linear model and directly incorporates dependencies between gene sets related to

SUBMITTER: Jablonski KP 

PROVIDER: S-EPMC10471899 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature