Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (182K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (81)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Huala, E.
Right arrow Articles by Rhee, S. Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Huala, E.
Right arrow Articles by Rhee, S. Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2001, Vol. 29, No. 1 102-105
© 2001 Oxford University Press

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

Eva Huala1,*, Allan W. Dickerman2, Margarita Garcia-Hernandez1, Danforth Weems2, Leonore Reiser1, Frank LaFond2, David Hanley2, Donald Kiphart2, Mingzhe Zhuang2, Wen Huang1,2, Lukas A. Mueller1, Debika Bhattacharyya1, Devaki Bhaya1, Bruno W. Sobral2, William Beavis2, David W. Meinke3, Christopher D. Town4, Chris Somerville1 and Seung Yon Rhee1

1Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA, 2National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA, 3Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA and 4The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).

* To whom correspondence should be addressed. Tel: +1 650 325 1521; Fax: +1 650 325 6857; Email: huala{at}acoma.stanford.edu Present addresses: Allan W. Dickerman, Virginia Bioinformatics Institute (0477), 1750 Kraft Drive, Corporate Research Center Building 10, Suite 1400, Blacksburg, VA 24061, USA Donald Kiphart, Prediction Company, 236 Montezuma Avenue, Santa Fe, NM 87501, USA Mingzhe Zhuang, Sugen, Inc., 230 East Grand Avenue, South San Francisco, CA 94080-4811, USA


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome ResHome page
H. Tang, X. Wang, J. E. Bowers, R. Ming, M. Alam, and A. H. Paterson
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
Genome Res., December 1, 2008; 18(12): 1944 - 1954.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Cui, P. Li, G. Li, F. Xu, C. Zhao, Y. Li, Z. Yang, G. Wang, Q. Yu, Y. Li, et al.
AtPID: Arabidopsis thaliana protein interactome database an integrative platform for plant systems biology
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D999 - D1008.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. L. Heazlewood, P. Durek, J. Hummel, J. Selbig, W. Weckwerth, D. Walther, and W. X. Schulze
PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D1015 - D1021.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
J. Kapteyn, A. V. Qualley, Z. Xie, E. Fridman, N. Dudareva, and D. R. Gang
Evolution of Cinnamate/p-Coumarate Carboxyl Methyltransferases and Their Role in the Biosynthesis of Methylcinnamate
PLANT CELL, October 1, 2007; 19(10): 3212 - 3229.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
K. Hori and Y. Watanabe
Context Analysis of Termination Codons in mRNA that are Recognized by Plant NMD
Plant Cell Physiol., July 1, 2007; 48(7): 1072 - 1078.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
M. Jaquinod, F. Villiers, S. Kieffer-Jaquinod, V. Hugouvieux, C. Bruley, J. Garin, and J. Bourguignon
A Proteomics Dissection of Arabidopsis thaliana Vacuoles Isolated from Cell Culture
Mol. Cell. Proteomics, March 1, 2007; 6(3): 394 - 412.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
B. P. Cusack and K. H. Wolfe
Changes in Alternative Splicing of Human and Mouse Genes Are Accompanied by Faster Evolution of Constitutive Exons
Mol. Biol. Evol., November 1, 2005; 22(11): 2198 - 2208.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Yan, D. Yoo, T. Z. Berardini, L. A. Mueller, D. C. Weems, S. Weng, J. M. Cherry, and S. Y. Rhee
PatMatch: a program for finding patterns in peptide and nucleotide sequences
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W262 - W266.
[Abstract] [Full Text] [PDF]

Home page
 J BiochemHome page
G. V. HarshaRani, S. J. Vayttaden, and U. S. Bhalla
Electronic Data Sources for Kinetic Models of Cell Signaling
J. Biochem., June 1, 2005; 137(6): 653 - 657.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
K. A.T. Silverstein, M. A. Graham, T. D. Paape, and K. A. VandenBosch
Genome Organization of More Than 300 Defensin-Like Genes in Arabidopsis
Plant Physiology, June 1, 2005; 138(2): 600 - 610.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
R. J. GRAINGER and J. D. BEGGS
Prp8 protein: At the heart of the spliceosome
RNA, May 1, 2005; 11(5): 533 - 557.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
A. Adai, C. Johnson, S. Mlotshwa, S. Archer-Evans, V. Manocha, V. Vance, and V. Sundaresan
Computational prediction of miRNAs in Arabidopsis thaliana
Genome Res., January 1, 2005; 15(1): 78 - 91.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
E. Bonnet, J. Wuyts, P. Rouze, and Y. Van de Peer
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes
PNAS, August 3, 2004; 101(31): 11511 - 11516.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Kankainen and L. Holm
POBO, transcription factor binding site verification with bootstrapping
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W222 - W229.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. A. Graham, K. A.T. Silverstein, S. B. Cannon, and K. A. VandenBosch
Computational Identification and Characterization of Novel Genes from Legumes
Plant Physiology, July 1, 2004; 135(3): 1179 - 1197.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. Vanstraelen, J. A. Torres Acosta, L. De Veylder, D. Inze, and D. Geelen
A Plant-Specific Subclass of C-Terminal Kinesins Contains a Conserved A-Type Cyclin-Dependent Kinase Site Implicated in Folding and Dimerization
Plant Physiology, July 1, 2004; 135(3): 1417 - 1429.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
C.-P. Lai, C.-L. Lee, P.-H. Chen, S.-H. Wu, C.-C. Yang, and J.-F. Shaw
Molecular Analyses of the Arabidopsis TUBBY-Like Protein Gene Family
Plant Physiology, April 1, 2004; 134(4): 1586 - 1597.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
A. Lorence, B. I. Chevone, P. Mendes, and C. L. Nessler
myo-Inositol Oxygenase Offers a Possible Entry Point into Plant Ascorbate Biosynthesis
Plant Physiology, March 1, 2004; 134(3): 1200 - 1205.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Guo, S. Hua, X. Ji, and Z. Sun
DBSubLoc: database of protein subcellular localization
Nucleic Acids Res., January 1, 2004; 32(90001): D122 - 124.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Schoof, R. Ernst, V. Nazarov, L. Pfeifer, H.-W. Mewes, and K. F. X. Mayer
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics
Nucleic Acids Res., January 1, 2004; 32(90001): D373 - 376.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
P. Windels, S. De Buck, E. Van Bockstaele, M. De Loose, and A. Depicker
T-DNA Integration in Arabidopsis Chromosomes. Presence and Origin of Filler DNA Sequences
Plant Physiology, December 1, 2003; 133(4): 2061 - 2068.
[Abstract] [Full Text]

Home page
 Genome ResHome page
L. J. Jensen, D. W. Ussery, and S. Brunak
Functionality of System Components: Conservation of Protein Function in Protein Feature Space
Genome Res., November 1, 2003; 13(11): 2444 - 2449.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. Baumgarten, S. Cannon, R. Spangler, and G. May
Genome-Level Evolution of Resistance Genes in Arabidopsis thaliana
Genetics, September 1, 2003; 165(1): 309 - 319.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
L. A. Mueller, P. Zhang, and S. Y. Rhee
AraCyc: A Biochemical Pathway Database for Arabidopsis
Plant Physiology, June 1, 2003; 132(2): 453 - 460.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
X. Pan, H. Liu, J. Clarke, J. Jones, M. Bevan, and L. Stein
ATIDB: Arabidopsis thaliana insertion database
Nucleic Acids Res., February 15, 2003; 31(4): 1245 - 1251.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
D. W. Meinke, L. K. Meinke, T. C. Showalter, A. M. Schissel, L. A. Mueller, and I. Tzafrir
A Sequence-Based Map of Arabidopsis Genes with Mutant Phenotypes
Plant Physiology, February 1, 2003; 131(2): 409 - 418.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Tzafrir, A. Dickerman, O. Brazhnik, Q. Nguyen, J. McElver, C. Frye, D. Patton, and D. Meinke
The Arabidopsis SeedGenes Project
Nucleic Acids Res., January 1, 2003; 31(1): 90 - 93.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Y. Rhee, W. Beavis, T. Z. Berardini, G. Chen, D. Dixon, A. Doyle, M. Garcia-Hernandez, E. Huala, G. Lander, M. Montoya, et al.
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
Nucleic Acids Res., January 1, 2003; 31(1): 224 - 228.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
G. TAYLOR
Populus: Arabidopsis for Forestry. Do We Need a Model Tree?
Ann. Bot., December 1, 2002; 90(6): 681 - 689.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Samson, V. Brunaud, S. Balzergue, B. Dubreucq, L. Lepiniec, G. Pelletier, M. Caboche, and A. Lecharny
FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants
Nucleic Acids Res., January 1, 2002; 30(1): 94 - 97.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. G. Gilbert
euGenes: a eukaryote genome information system
Nucleic Acids Res., January 1, 2002; 30(1): 145 - 148.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
K. A. Lease, J. Wen, J. Li, J. T. Doke, E. Liscum, and J. C. Walker
A Mutant Arabidopsis Heterotrimeric G-Protein {beta} Subunit Affects Leaf, Flower, and Fruit Development
PLANT CELL, December 1, 2001; 13(12): 2631 - 2641.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
T. G. O. Consortium
Creating the Gene Ontology Resource: Design and Implementation
Genome Res., August 1, 2001; 11(8): 1425 - 1433.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.