Detection of interacting transcription factors in human tissues using predicted DNA binding affinity.

ABSTRACT:

Background

Tissue-specific gene expression is generally regulated by combinatorial interactions among transcription factors (TFs) which bind to the DNA. Despite this known fact, previous discoveries of the mechanism that controls gene expression usually consider only a single TF.

Results

We provide a prediction of interacting TFs in 22 human tissues based on their DNA-binding affinity in promoter regions. We analyze all possible pairs of 130 vertebrate TFs from the JASPAR database. First, all human promoter regions are scanned for single TF-DNA binding affinities with TRAP and for each TF a ranked list of all promoters ordered by the binding affinity is created. We then study the similarity of the ranked lists and detect candidates for TF-TF interaction by applying a partial

SUBMITTER: Mysickova A 

PROVIDER: S-EPMC3583127 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature