Assessing computational methods for transcription factor target gene identification based on ChIP-seq data.

ABSTRACT: Chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) has great potential for elucidating transcriptional networks, by measuring genome-wide binding of transcription factors (TFs) at high resolution. Despite the precision of these experiments, identification of genes directly regulated by a TF (target genes) is not trivial. Numerous target gene scoring methods have been used in the past. However, their suitability for the task and their performance remain unclear, because a thorough comparative assessment of these methods is still lacking. Here we present a systematic evaluation of computational methods for defining TF targets based on ChIP-seq data. We validated predictions based on 68 ChIP-seq studies using a wide range of genomic expression data and functional informatio

SUBMITTER: Sikora-Wohlfeld W 

PROVIDER: S-EPMC3837635 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature