rTRM-web: a web tool for predicting transcriptional regulatory modules for ChIP-seq-ed transcription factors

Abstract

Transcription factors (TFs) bind to specific DNA regions, although their binding specificities cannot account for their cell type-specific functions. It has been shown in well-studied systems that TFs combine with co-factors into transcriptional regulatory modules (TRMs), which endow them with cell type-specific functions and additional modes of regulation. Therefore, the prediction of TRMs can provide fundamental mechanistic insights, especially when experimental data are limiting or when no regulatory proteins have been identified. Our method rTRM predicts TRMs by integrating genomic information from TF ChIP-seq data, cell type-specific gene expression and protein-protein interaction data. Here we present a freely available web interface to rTRM (http://www.rTRM.org/) supporting all the options originally described for rTRM while featuring flexible display and network calculation parameters, publication-quality figures as well as annotated information on the list of genes constituting the TRM.

Keywords: ChIP-seq; Network; Protein–protein interactions; Transcription factor; Transcriptional regulatory module.