ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.

ABSTRACT:

Motivation

Experiments such as ChIP-chip, ChIP-seq, ChIP-PET and DamID (the four methods referred herein as ChIP-X) are used to profile the binding of transcription factors to DNA at a genome-wide scale. Such experiments provide hundreds to thousands of potential binding sites for a given transcription factor in proximity to gene coding regions.

Results

In order to integrate data from such studies and utilize it for further biological discovery, we collected interactions from such experiments to construct a mammalian ChIP-X database. The database contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes. We used the database to analyze mRNA expression data where we perform gene-list enric

SUBMITTER: Lachmann A 

PROVIDER: S-EPMC2944209 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature