Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments.

ABSTRACT: Recent advances in technology have led to a dramatic increase in the number of available transcription factor ChIP-seq and ChIP-chip data sets. Understanding the motif content of these data sets is an important step in understanding the underlying mechanisms of regulation. Here we provide a systematic motif analysis for 427 human ChIP-seq data sets using motifs curated from the literature and also discovered de novo using five established motif discovery tools. We use a systematic pipeline for calculating motif enrichment in each data set, providing a principled way for choosing between motif variants found in the literature and for flagging potentially problematic data sets. Our analysis confirms the known specificity of 41 of the 56 analyzed factor groups and reveals motifs of potential

SUBMITTER: Kheradpour P 

PROVIDER: S-EPMC3950668 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature