title: TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.
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).
authors.affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
authors.forename: Fang
authors.initials: F
authors.lastname: Zhao
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Xuan
authors.forename: Lihua
authors.initials: L
authors.lastname: Liu
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001665:Binding Sites; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D005786:Gene Expression Regulation; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D009369:Neoplasms / Q000235:genetics; D011401:Promoter Regions, Genetic; D051381:Rats; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors