AGRIS: the Arabidopsis Gene Regulatory Information Server, an Update

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2010 Nov 10

PMID 21059685

Citations 180

Authors

Alper Yilmaz

Maria Katherine Mejia-Guerra

Kyle Kurz

Xiaoyu Liang

Lonnie Welch

Erich Grotewold

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Insights into genetics of floral development in Amborella trichopoda Baill. through genome-wide survey and expression analysis of MADS-Box transcription factors.

Parajuli S, Adhikari B, Nepal M Sci Rep. 2025; 15(1):5297.

PMID: 39939686 PMC: 11822109. DOI: 10.1038/s41598-025-88880-x.

Workflow to Select Functional Promoter DNA Baits and Screen Arrayed Gene Libraries in Yeast.

Fananas-Pueyo I, Anhel A, Goni-Moreno A, Onate-Sanchez L, Carrera-Castano G Curr Protoc. 2024; 4(11):e70059.

PMID: 39570200 PMC: 11580771. DOI: 10.1002/cpz1.70059.

Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA.

Zhang L, Jiang G, Wang X, Bai Y, Zhang P, Liu J Int J Mol Sci. 2024; 25(13).

PMID: 38999994 PMC: 11241592. DOI: 10.3390/ijms25136885.

Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis.

Del Toro-De Leon G, van Boven J, Santos-Gonzalez J, Jiao W, Peng H, Schneeberger K Nucleic Acids Res. 2024; 52(15):8833-8848.

PMID: 38967011 PMC: 11347142. DOI: 10.1093/nar/gkae572.

Recent advances in exploring transcriptional regulatory landscape of crops.

Huo Q, Song R, Ma Z Front Plant Sci. 2024; 15:1421503.

PMID: 38903438 PMC: 11188431. DOI: 10.3389/fpls.2024.1421503.

References

Cline M, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C . Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82. PMC: 3685583. DOI: 10.1038/nprot.2007.324. View

Davuluri R, Sun H, Palaniswamy S, Matthews N, Molina C, Kurtz M . AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics. 2003; 4:25. PMC: 166152. DOI: 10.1186/1471-2105-4-25. View

Koornneef M, Meinke D . The development of Arabidopsis as a model plant. Plant J. 2010; 61(6):909-21. DOI: 10.1111/j.1365-313X.2009.04086.x. View

Alonso J, Stepanova A, Leisse T, Kim C, Chen H, Shinn P . Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science. 2003; 301(5633):653-7. DOI: 10.1126/science.1086391. View

Swarbreck D, Wilks C, Lamesch P, Berardini T, Garcia-Hernandez M, Foerster H . The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 2007; 36(Database issue):D1009-14. PMC: 2238962. DOI: 10.1093/nar/gkm965. View

Schlitt T, Brazma A . Current approaches to gene regulatory network modelling. BMC Bioinformatics. 2007; 8 Suppl 6:S9. PMC: 1995542. DOI: 10.1186/1471-2105-8-S6-S9. View

Sun H, Davuluri R . Java-based application framework for visualization of gene regulatory region annotations. Bioinformatics. 2004; 20(5):727-34. DOI: 10.1093/bioinformatics/btg476. View

Oh E, Kang H, Yamaguchi S, Park J, Lee D, Kamiya Y . Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis. Plant Cell. 2009; 21(2):403-19. PMC: 2660632. DOI: 10.1105/tpc.108.064691. View

Palaniswamy S, James S, Sun H, Lamb R, Davuluri R, Grotewold E . AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiol. 2006; 140(3):818-29. PMC: 1400579. DOI: 10.1104/pp.105.072280. View

10.

Lichtenberg J, Yilmaz A, Welch J, Kurz K, Liang X, Drews F . The word landscape of the non-coding segments of the Arabidopsis thaliana genome. BMC Genomics. 2009; 10:463. PMC: 2770528. DOI: 10.1186/1471-2164-10-463. View

11.

Perez-Rodriguez P, Riano-Pachon D, Correa L, Rensing S, Kersten B, Mueller-Roeber B . PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 2009; 38(Database issue):D822-7. PMC: 2808933. DOI: 10.1093/nar/gkp805. View

12.

Stein L, Mungall C, Shu S, Caudy M, Mangone M, Day A . The generic genome browser: a building block for a model organism system database. Genome Res. 2002; 12(10):1599-610. PMC: 187535. DOI: 10.1101/gr.403602. View

13.

Spannagl M, Noubibou O, Haase D, Yang L, Gundlach H, Hindemitt T . MIPSPlantsDB--plant database resource for integrative and comparative plant genome research. Nucleic Acids Res. 2007; 35(Database issue):D834-40. PMC: 1899105. DOI: 10.1093/nar/gkl945. View

14.

Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K . ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res. 2008; 37(Database issue):D987-91. PMC: 2686564. DOI: 10.1093/nar/gkn807. View

15.

OConnor T, Dyreson C, Wyrick J . Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. Bioinformatics. 2005; 21(24):4411-3. DOI: 10.1093/bioinformatics/bti714. View

16.

Moreno-Risueno M, Busch W, Benfey P . Omics meet networks - using systems approaches to infer regulatory networks in plants. Curr Opin Plant Biol. 2009; 13(2):126-31. PMC: 2862083. DOI: 10.1016/j.pbi.2009.11.005. View