Predicting tissue specific transcription factor binding sites.

ABSTRACT:

Background

Studies of gene regulation often utilize genome-wide predictions of transcription factor (TF) binding sites. Most existing prediction methods are based on sequence information alone, ignoring biological contexts such as developmental stages and tissue types. Experimental methods to study in vivo binding, including ChIP-chip and ChIP-seq, can only study one transcription factor in a single cell type and under a specific condition in each experiment, and therefore cannot scale to determine the full set of regulatory interactions in mammalian transcriptional regulatory networks.

Results

We developed a new computational approach, PIPES, for predicting tissue-specific TF binding. PIPES integrates in vitro protein binding microarrays (PBMs), sequence conservation and ti

SUBMITTER: Zhong S 

PROVIDER: S-EPMC3898213 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature