Transcription factor site dependencies in human, mouse and rat genomes.

ABSTRACT:

Background

It is known that transcription factors frequently act together to regulate gene expression in eukaryotes. In this paper we describe a computational analysis of transcription factor site dependencies in human, mouse and rat genomes.

Results

Our approach for quantifying tendencies of transcription factor binding sites to co-occur is based on a binding site scoring function which incorporates dependencies between positions, the use of information about the structural class of each transcription factor (major/minor groove binder), and also considered the possible implications of varying GC content of the sequences. Significant tendencies (dependencies) have been detected by non-parametric statistical methodology (permutation tests). Evaluation of obtained results has

SUBMITTER: Tomovic A 

PROVIDER: S-EPMC2770556 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature