Nucleic Acids Research Advance Access originally published online on October 15, 2008
Nucleic Acids Research 2009 37(Database issue):D66-D71; doi:10.1093/nar/gkn731
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Nucleic Acids Research, 2009, Vol. 37, Database issue D66-D71
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
PTM-Switchboard—a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes
1Penn Center for Bioinformatics, Department of Genetics and 2Department of Computer Science, University of Pennsylvania, Philadelphia, PA, USA
*To whom correspondence should be addressed. Tel: +1 215 746 5145; Fax: +1 215 573 3111; Email: loganje{at}mail.med.upenn.edu
Correspondence may also be addressed to Sridhar Hannenhalli. Tel: +1 215 746 8683; Fax: +1 215 573 3111; Email: sridharh{at}pcbi.upenn.edu
Received August 14, 2008. Revised September 23, 2008. Accepted October 1, 2008.
Gene transcription is largely regulated by sequence-specific transcription factors (TFs). The TF activity is significantly regulated by its posttranslational modifications (PTMs). TF-PTMs serve as ‘molecular switchboards’ that map multiple upstream signaling events, in response to various environmental perturbations, to the downstream transcriptional events. While many instances of TF-PTMs and their effect on gene regulation have been experimentally determined, a systematic meta-analysis or a quantitative model-based investigation of this process has not been undertaken. A prerequisite to such analyses is a database of known instances of TF-PTMs affecting transcriptional regulation. The PTM-Switchboard database meets this need by cataloging such instances in the model system Saccharomyces cerevisiae. The database stores triplets of genes such that the ability of one gene (TF) to regulate a target gene is dependent on one or more PTMs catalyzed by a third gene (modifying enzyme). The database currently includes a large sample of experimentally characterized instances curated from the literature. In addition to providing a framework for searching and analyzing the data, the database will serve to benchmark computational methods. In the future, the database will be expanded to mammalian organisms, and will also include triplets predicted from computational approaches. The database can be accessed at http://cagr.pcbi.upenn.edu/PTMswitchboard.