Broad-Enrich: functional interpretation of large sets of broad genomic regions.

ABSTRACT:

Motivation

Functional enrichment testing facilitates the interpretation of Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) data in terms of pathways and other biological contexts. Previous methods developed and used to test for key gene sets affected in ChIP-seq experiments treat peaks as points, and are based on the number of peaks associated with a gene or a binary score for each gene. These approaches work well for transcription factors, but histone modifications often occur over broad domains, and across multiple genes.

Results

To incorporate the unique properties of broad domains into functional enrichment testing, we developed Broad-Enrich, a method that uses the proportion of each gene's locus covered by a peak. We show that our method

SUBMITTER: Cavalcante RG 

PROVIDER: S-EPMC4147897 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature