TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies

Zhao, F., Xuan, Z., Liu, L., Zhang, M. Q. (January 2005) TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res, 33 (Databa). D103-107. ISSN 1362-4962 (Electronic)

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URL: http://www.pubmedcentral.nih.gov/articlerender.fcg...
DOI: 10.1093/nar/gki004

Abstract

In order to understand gene regulation, accurate and comprehensive knowledge of transcriptional regulatory elements is essential. Here, we report our efforts in building a mammalian Transcriptional Regulatory Element Database (TRED) with associated data analysis functions. It collects cis- and trans-regulatory elements and is dedicated to easy data access and analysis for both single-gene-based and genome-scale studies. Distinguishing features of TRED include: (i) relatively complete genome-wide promoter annotation for human, mouse and rat; (ii) availability of gene transcriptional regulation information including transcription factor binding sites and experimental evidence; (iii) data accuracy is ensured by hand curation; (iv) efficient user interface for easy and flexible data retrieval; and (v) implementation of on-the-fly sequence analysis tools. TRED can provide good training datasets for further genome-wide cis-regulatory element prediction and annotation, assist detailed functional studies and facilitate the decipher of gene regulatory networks (http://rulai.cshl.edu/TRED).

Item Type: Paper
Uncontrolled Keywords: Animals Binding Sites Computational Biology Databases Nucleic Acid Gene Expression Regulation Genomics Humans Internet Mice Neoplasms genetics Promoter Regions genetics Rats Software Transcription Factors metabolism User-Computer Interface
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cis-regulatory elements
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 > Zheng lab
Depositing User: CSHL Librarian
Date: 1 January 2005
Date Deposited: 21 Dec 2011 18:54
Last Modified: 21 Dec 2011 18:54
URI: http://repository.cshl.edu/id/eprint/22743

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