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

Fang Zhao, Zhenyu Xuan, Lihua Liu, Michael Q. Zhang

Research output: Contribution to journalArticle

152 Scopus citations

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).

Original languageEnglish (US)
Pages (from-to)D103-D107
JournalNucleic acids research
Volume33
Issue numberDATABASE ISS.
DOIs
StatePublished - Jan 1 2005
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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