Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data.

ABSTRACT:

Background

Chromatin immunoprecipitation (ChIP) experiments are now the most comprehensive experimental approaches for mapping the binding of transcription factors (TFs) to their target genes. However, ChIP data alone is insufficient for identifying functional binding target genes of TFs for two reasons. First, there is an inherent high false positive/negative rate in ChIP-chip or ChIP-seq experiments. Second, binding signals in the ChIP data do not necessarily imply functionality.

Methods

It is known that ChIP-chip data and TF knockout (TFKO) data reveal complementary information on gene regulation. While ChIP-chip data can provide TF-gene binding pairs, TFKO data can provide TF-gene regulation pairs. Therefore, we propose a novel network approach for identifying functional

SUBMITTER: Yang TH 

PROVIDER: S-EPMC4029220 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature