title: Regulating the regulators: modulators of transcription factor activity.
abstract: Gene transcription is largely regulated by DNA-binding transcription factors (TFs). However, the TF activity itself is modulated via, among other things, post-translational modifications (PTMs) by specific modification enzymes in response to cellular stimuli. TF-PTMs thus serve as "molecular switchboards" that map upstream signaling events to the downstream transcriptional events. An important long-term goal is to obtain a genome-wide map of "regulatory triplets" consisting of a TF, target gene, and a modulator gene that specifically modulates the regulation of the target gene by the TF. A variety of genome-wide data sets can be exploited by computational methods to obtain a rough map of regulatory triplets, which can guide directed experiments. However, a prerequisite to developing such computational tools is a systematic catalog of known instances of regulatory triplets. We first describe PTM-Switchboard, a recent database that stores triplets of genes such that the ability of one gene (the TF) to regulate a target gene is dependent on one or more PTMs catalyzed by a third gene, the modifying enzyme. We also review current computational approaches to infer regulatory triplets from genome-wide data sets and conclude with a discussion of potential future research. PTM-Switchboard is accessible at http://cagr.pcbi.upenn.edu/PTMswitchboard /
authors.affiliation: Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA. loganje@mail.med.upenn.edu
authors.forename: Logan
authors.initials: L
authors.lastname: Everett
authors.forename: Matthew
authors.initials: M
authors.lastname: Hansen
authors.forename: Sridhar
authors.initials: S
authors.lastname: Hannenhalli
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008954:Models, Biological; D011499:Protein Processing, Post-Translational; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors