Nucleic Acids Research Advance Access originally published online on December 11, 2007
Nucleic Acids Research 2008 36(Database issue):D88-D92; doi:10.1093/nar/gkm964
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Nucleic Acids Research, 2008, Vol. 36, Database issue D88-D92
© 2007 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 |
DBD––taxonomically broad transcription factor predictions: new content and functionality
1MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK and 2Department of Developmental Biology, Stanford University Medical Center, 279 Campus Drive, Stanford, CA 94305-5329, USA
*To whom correspondence should be addressed. Tel: +44 (0)1223 402479; Fax: +44 (0)1223 213556; Email: dbd{at}mrc-lmb.cam.ac.uk
Received September 14, 2007. Revised October 16, 2007. Accepted October 17, 2007.
DNA-binding domain (DBD) is a database of predicted sequence-specific DNA-binding transcription factors (TFs) for all publicly available proteomes. The proteomes have increased from 150 in the initial version of DBD to over 700 in the current version. All predicted TFs must contain a significant match to a hidden Markov model representing a sequence-specific DNA-binding domain family. Access to TF predictions is provided through http://transcriptionfactor.org, where new search options are now provided such as searching by gene names in model organisms, searching for all proteins in a particular DBD family and specific organism. We illustrate the application of this type of search facility by contrasting trends of DBD family occurrence throughout the tree of life, highlighting the clear partition between eukaryotic and prokaryotic DBD expansions. The website content has been expanded to include dedicated pages for each TF containing domain assignment details, gene names, links to external databases and links to TFs with similar domain arrangements. We compare the increase in number of predicted TFs with proteome size in eukaryotes and prokaryotes. Eukaryotes follow a slower rate of increase in TFs than prokaryotes, which could be due to the presence of splice variants or an increase in combinatorial control.
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