Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions.

ABSTRACT: Gene set enrichment (GSE) testing enhances the biological interpretation of ChIP-seq data and other large sets of genomic regions. Our group has previously introduced two GSE methods for genomic regions: ChIP-Enrich for narrow regions and Broad-Enrich for broad regions. Here, we introduce Poly-Enrich, which has wider applicability, additional capabilities and models the number of peaks assigned to a gene using a generalized additive model with a negative binomial family to determine gene set enrichment, while adjusting for gene locus length. As opposed to ChIP-Enrich, Poly-Enrich works well even when nearly all genes have a peak, illustrated by using Poly-Enrich to characterize pathways and types of genic regions enriched with different families of repetitive elements. By comparing Poly-En

SUBMITTER: Lee CT 

PROVIDER: S-EPMC7003681 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature