ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data.

ABSTRACT:

Background

ChIP-Seq is a powerful tool for identifying the interaction between genomic regulators and their bound DNAs, especially for locating transcription factor binding sites. However, high cost and high rate of false discovery of transcription factor binding sites identified from ChIP-Seq data significantly limit its application.

Results

Here we report a new algorithm, ChIP-PaM, for identifying transcription factor target regions in ChIP-Seq datasets. This algorithm makes full use of a protein-DNA binding pattern by capitalizing on three lines of evidence: 1) the tag count modelling at the peak position, 2) pattern matching of a specific tag count distribution, and 3) motif searching along the genome. A novel data-based two-step eFDR procedure is proposed to integrate t

SUBMITTER: Wu S 

PROVIDER: S-EPMC2893127 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature