A protein-protein interaction guided method for competitive transcription factor binding improves target predictions.

ABSTRACT: An important milestone in revealing cells' functions is to build a comprehensive understanding of transcriptional regulation processes. These processes are largely regulated by transcription factors (TFs) binding to DNA sites. Several TF binding site (TFBS) prediction methods have been developed, but they usually model binding of a single TF at a time albeit few methods for predicting binding of multiple TFs also exist. In this article, we propose a probabilistic model that predicts binding of several TFs simultaneously. Our method explicitly models the competitive binding between TFs and uses the prior knowledge of existing protein-protein interactions (PPIs), which mimics the situation in the nucleus. Modeling DNA binding for multiple TFs improves the accuracy of binding site prediction

SUBMITTER: Laurila K 

PROVIDER: S-EPMC2794167 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature