Probing transcription factor combinatorics in different promoter classes and in enhancers.

ABSTRACT:

Background

In eukaryotic cells, transcription factors (TFs) are thought to act in a combinatorial way, by competing and collaborating to regulate common target genes. However, several questions remain regarding the conservation of these combinations among different gene classes, regulatory regions and cell types.

Results

We propose a new approach named TFcoop to infer the TF combinations involved in the binding of a target TF in a particular cell type. TFcoop aims to predict the binding sites of the target TF upon the nucleotide content of the sequences and of the binding affinity of all identified cooperating TFs. The set of cooperating TFs and model parameters are learned from ChIP-seq data of the target TF. We used TFcoop to investigate the TF combinations involved in the

SUBMITTER: Vandel J 

PROVIDER: S-EPMC6359851 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature