Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.

ABSTRACT:

Background

Chromatin immunoprecipitation (ChIP) coupled to high-throughput sequencing (ChIP-Seq) techniques can reveal DNA regions bound by transcription factors (TF). Analysis of the ChIP-Seq regions is now a central component in gene regulation studies. The need remains strong for methods to improve the interpretation of ChIP-Seq data and the study of specific TF binding sites (TFBS).

Results

We introduce a set of methods to improve the interpretation of ChIP-Seq data, including the inference of mediating TFs based on TFBS motif over-representation analysis and the subsequent study of spatial distribution of TFBSs. TFBS over-representation analysis applied to ChIP-Seq data is used to detect which TFBSs arise more frequently than expected by chance. Visualization of over-re

SUBMITTER: Worsley Hunt R 

PROVIDER: S-EPMC4082612 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature