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PMID: 16524982 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks.

Plant physiology ·Vol. 140 ·No. 3 ·2006-03-00 ·Pages 818-29

Palaniswamy SK, James S, Sun H, Lamb RS, Davuluri RV, Grotewold E

Abstract

Gene regulatory pathways converge at the level of transcription, where interactions among regulatory genes and between regulators and target genes result in the establishment of spatiotemporal patterns of gene expression. The growing identification of direct target genes for key transcription factors (TFs) through traditional and high-throughput experimental approaches has facilitated the elucidation of regulatory networks at the genome level. To integrate this information into a Web-based knowledgebase, we have developed the Arabidopsis Gene Regulatory Information Server (AGRIS). AGRIS, which contains all Arabidopsis (Arabidopsis thaliana) promoter sequences, TFs, and their target genes and functions, provides the scientific community with a platform to establish regulatory networks. AGRIS currently houses three linked databases: AtcisDB (Arabidopsis thaliana cis-regulatory database), AtTFDB (Arabidopsis thaliana transcription factor database), and AtRegNet (Arabidopsis thaliana regulatory network). AtTFDB contains 1,690 Arabidopsis TFs and their sequences (protein and DNA) grouped into 50 (October 2005) families with information on available mutants in the corresponding genes. AtcisDB consists of 25,806 (September 2005) promoter sequences of annotated Arabidopsis genes with a description of putative cis-regulatory elements. AtRegNet links, in direct interactions, several hundred genes with the TFs that control their expression. The current release of AtRegNet contains a total of 187 (September 2005) direct targets for 66 TFs. AGRIS can be accessed at http://Arabidopsis.med.ohio-state.edu.

MeSH Terms
Arabidopsis/genetics Computational Biology/methods Databases, Genetic Flowers/genetics,growth & development Gene Expression Regulation, Plant Internet Promoter Regions, Genetic Transcription Factors/metabolism,physiology
Chemicals
Transcription Factors
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Palaniswamy Saranyan K
Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics , The Ohio State University, Columbus, 43210, USA.
James Stephen
Sun Hao
Lamb Rebecca S
Davuluri Ramana V
Grotewold Erich
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Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
0032-0889
DOI
10.1104/pp.105.072280
Published
2006-03-00
Pages
818-29
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC1400579
Subset
IM
External Links
PubMed source DOI: 10.1104/pp.105.072280 PMC Full Text View journal details
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