TRED: a transcriptional regulatory element database, new entries and other development

Jiang, C., Xuan, Z. Y., Zhao, F., Zhang, M. Q. (2007) TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res, 35 (Databa). D137-D140. ISSN 0305-1048

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URL: https://www.ncbi.nlm.nih.gov/pubmed/17202159
DOI: 10.1093/nar/gkl1041

Abstract

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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > databases > database optimization
bioinformatics > genomics and proteomics > Mapping and Rendering
bioinformatics > genomics and proteomics > databases > databases
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date Deposited: 14 Nov 2011 19:51
Last Modified: 28 Mar 2018 14:33
PMCID: PMC1899102
Related URLs:
URI: http://repository.cshl.edu/id/eprint/23054

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