title: 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.
authors.affiliation: School of Computer Science and Engineering, Beijing University of Aeronautics and Astronautics (BUAA), Building 16, Min'an Street, Dong Cheng District, Beijing 100007, China.
authors.forename: Fengkai
authors.initials: F
authors.lastname: Liu
authors.affiliation: Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom. Electronic address: diego.miranda-saavedra@ncl.ac.UK.
authors.forename: Diego
authors.initials: D
authors.lastname: Miranda-Saavedra
mesh_terms: D030562:Databases, Protein; D005786:Gene Expression Regulation / Q000502:physiology; D020407:Internet; D008954:Models, Biological; D020218:Response Elements / Q000502:physiology*; D012984:Software; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D014157:Transcription Factors
keywords: ChIP-seq; Network; Protein–protein interactions; Transcription factor; Transcriptional regulatory module