Nucleic Acids Research, 2007, Vol. 35, Database issue D137-D140
© 2006 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.
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TRED: a transcriptional regulatory element database, new entries and other development
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY 11724, USA
*To whom correspondence should be addressed. Tel: +1 516 367 8393; Fax: +1 516 367 8461; Email: mzhang{at}cshl.edu
Received September 8, 2006. Revised November 3, 2006. Accepted November 3, 2006.
Transcriptional factors (TFs) and many of their target genes are involved in gene regulation at the level of transcription. To decipher gene regulatory networks (GRNs) we require a comprehensive and accurate knowledge of transcriptional regulatory elements. TRED (http://rulai.cshl.edu/TRED) was designed as a resource for gene regulation and function studies. It collects mammalian cis- and trans-regulatory elements together with experimental evidence. All the regulatory elements were mapped on to the assembled genomes. In this new release, we included a total of 36 TF families involved in cancer. Accordingly, the number of target promoters and genes for TF families has increased dramatically. There are 11 660 target genes (7479 in human, 2691 in mouse and 1490 in rat) and 14 908 target promoters (10 225 in human, 2985 in mouse and 1698 in rat). Additionally, we constructed GRNs for each TF family by connecting the TF–target gene pairs. Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research.
Present addresses: C. Jiang, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, PO Box 980126, Richmond, VA 23298, USA
F. Zhao, Global Business Analytics, Global Pharmaceutical Business, Schering-Plough, Kenilworth, NJ 07033, USA
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