AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

The Arabidopsis Gene Regulatory Information Server (AGRIS; http://arabidopsis.med.ohio-state.edu/) provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively. In addition to significant contributions in the identification of the entire set of TF–DNA interactions, which are the key to understand the gene regulatory networks that govern Arabidopsis gene expression, tools recently incorporated into AGRIS include the complete set of words length 5–15 present in the Arabidopsis genome and the integration of AtRegNet with visualization tools, such as the recently developed ReIN application. All the information in AGRIS is publicly available and downloadable upon registration.

[1]  Birgit Kersten,et al.  PlnTFDB: updated content and new features of the plant transcription factor database , 2009, Nucleic Acids Res..

[2]  M. Schmid,et al.  Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana , 2003, Science.

[3]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): gene structure and function annotation , 2007, Nucleic Acids Res..

[4]  Kengo Kinoshita,et al.  ATTED-II provides coexpressed gene networks for Arabidopsis , 2008, Nucleic Acids Res..

[5]  Wolfgang Busch,et al.  Omics meet networks - using systems approaches to infer regulatory networks in plants. , 2010, Current opinion in plant biology.

[6]  Saranyan K. Palaniswamy,et al.  AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks1[W][OA] , 2006, Plant Physiology.

[7]  Joshua D. Welch,et al.  The word landscape of the non-coding segments of the Arabidopsis thaliana genome , 2009, BMC Genomics.

[8]  M. Koornneef,et al.  The development of Arabidopsis as a model plant. , 2010, The Plant journal : for cell and molecular biology.

[9]  Li Yang,et al.  MIPSPlantsDB—plant database resource for integrative and comparative plant genome research , 2007, Nucleic Acids Res..

[10]  Alvis Brazma,et al.  Current approaches to gene regulatory network modelling , 2007, BMC Bioinformatics.

[11]  Ramana V. Davuluri,et al.  Java-based application framework for visualization of gene regulatory region annotations , 2004, Bioinform..

[12]  Michael L. Creech,et al.  Integration of biological networks and gene expression data using Cytoscape , 2007, Nature Protocols.

[13]  Ramana V. Davuluri,et al.  AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors , 2003, BMC Bioinformatics.

[14]  Curtis E. Dyreson,et al.  Genome analysis Athena : a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences , 2005 .

[15]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[16]  Doheon Lee,et al.  Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination in Arabidopsis[W] , 2009, The Plant Cell Online.