@inbook {14638,
	title = {Regulating the Regulators: Modulators of Transcription Factor Activity},
	booktitle = {Computational Biology of Transcription Factor BindingComputational Biology of Transcription Factor Binding},
	series = {Methods in Molecular Biology},
	volume = {674},
	year = {2010},
	month = {2010///},
	pages = {297 - 312},
	publisher = {Humana Press},
	organization = {Humana Press},
	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 {\textquotedblleft}molecular switchboards{\textquotedblright} that map upstream signaling events to the downstream transcriptional events. An important long-term goal is to obtain a genome-wide map of {\textquotedblleft}regulatory triplets{\textquotedblright} 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 /},
	isbn = {978-1-60761-854-6},
	url = {http://dx.doi.org/10.1007/978-1-60761-854-6_19},
	author = {Everett,Logan and Hansen,Matthew and Hannenhalli, Sridhar},
	editor = {Ladunga,Istvan}
}
