Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data

• DOI: 10.1371/journal.pcbi.1003342
• Publication Date: 2013-11-21T22:19:40Z
• Authors: Weronika Sikora-W...; Marit Ackermann; Eleni G. Christod...; Kalaimathy Singar...; Andreas Beyer
• Keywords: Chromatin immunoprecipitation; Identification

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 these experiments, identification genes directly regulated a TF (target genes) is not trivial. Numerous target gene scoring methods have been used in past. However, their suitability task and performance remain unclear, because thorough comparative assessment still lacking. Here we present systematic evaluation computational defining targets based on ChIP-seq data. We validated predictions 68 studies using wide range genomic expression data functional information. demonstrate that peak-to-gene assignment most crucial step correct prediction propose parameter-free method performing consistently across tests.