Skip Navigation



Nucleic Acids Research Advance Access published online on November 5, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm965
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (3349K) Freely available
Right arrow Screen PDF (458K) Freely available
Right arrowOA All Versions of this Article:
36/suppl_1/D1009    most recent
gkm965v1
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 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 Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Swarbreck, D.
Right arrow Articles by Huala, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Swarbreck, D.
Right arrow Articles by Huala, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

The Arabidopsis Information Resource (TAIR): gene structure and function annotation

David Swarbreck*, Christopher Wilks, Philippe Lamesch, Tanya Z. Berardini, Margarita Garcia-Hernandez, Hartmut Foerster, Donghui Li, Tom Meyer, Robert Muller, Larry Ploetz, Amie Radenbaugh, Shanker Singh, Vanessa Swing, Christophe Tissier, Peifen Zhang and Eva Huala

Carnegie Institution, Department of Plant Biology, 260 Panama St., Stanford, CA 94305, USA

*To whom correspondence should be addressed. Tel: +1 650 325 1521; Fax: +1 650 325 6857; Email: dswarbreck{at}stanford.edu

Received September 14, 2007. Revised October 16, 2007. Accepted October 17, 2007.

The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research community. New developments at TAIR include the addition of the GBrowse genome viewer to the TAIR site, a redesigned home page, navigation structure and portal pages to make the site more intuitive and easier to use, the launch of several TAIR web services and a new genome annotation release (TAIR7) in April 2007. A combination of manual and computational methods were used to generate this release, which contains 27 029 protein-coding genes, 3889 pseudogenes or transposable elements and 1123 ncRNAs (32 041 genes in all, 37 019 gene models). A total of 681 new genes and 1002 new splice variants were added. Overall, 10 098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release.


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
 Nucleic Acids ResHome page
J. Muller, D. Szklarczyk, P. Julien, I. Letunic, A. Roth, M. Kuhn, S. Powell, C. von Mering, T. Doerks, L. J. Jensen, et al.
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
Nucleic Acids Res., November 9, 2009; (2009) gkp951v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Ostlund, T. Schmitt, K. Forslund, T. Kostler, D. N. Messina, S. Roopra, O. Frings, and E. L. L. Sonnhammer
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
Nucleic Acids Res., November 5, 2009; (2009) gkp931v1.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. M. Flowers, Y. Hanzawa, M. C. Hall, R. C. Moore, and M. D. Purugganan
Population Genomics of the Arabidopsis thaliana Flowering Time Gene Network
Mol. Biol. Evol., November 1, 2009; 26(11): 2475 - 2486.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Perez-Rodriguez, D. M. Riano-Pachon, L. G. G. Correa, S. A. Rensing, B. Kersten, and B. Mueller-Roeber
PlnTFDB: updated content and new features of the plant transcription factor database
Nucleic Acids Res., October 25, 2009; (2009) gkp805v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. G. Soldatos, S. I. O'Donoghue, V. P. Satagopam, L. J. Jensen, N. P. Brown, A. Barbosa-Silva, and R. Schneider
Martini: using literature keywords to compare gene sets
Nucleic Acids Res., October 25, 2009; (2009) gkp876v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Mihara, T. Itoh, and T. Izawa
SALAD database: a motif-based database of protein annotations for plant comparative genomics
Nucleic Acids Res., October 23, 2009; (2009) gkp831v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
The UniProt Consortium
The Universal Protein Resource (UniProt) in 2010
Nucleic Acids Res., October 20, 2009; (2009) gkp846v1.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. Kinoshita and T. Obayashi
Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis
Bioinformatics, October 15, 2009; 25(20): 2677 - 2684.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
T. Obayashi and K. Kinoshita
Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression
DNA Res, October 1, 2009; 16(5): 249 - 260.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
C. Liang, L. Mao, D. Ware, and L. Stein
Evidence-based gene predictions in plant genomes
Genome Res., October 1, 2009; 19(10): 1912 - 1923.
[Abstract] [Full Text] [PDF]

Home page
 Mol PlantHome page
A. Brautigam and A. P.M. Weber
Proteomic Analysis of the Proplastid Envelope Membrane Provides Novel Insights into Small Molecule and Protein Transport across Proplastid Membranes
Mol Plant, August 25, 2009; (2009) ssp070v1.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
C. D. Leasure, H. Tong, G. Yuen, X. Hou, X. Sun, and Z.-H. He
ROOT UV-B SENSITIVE2 Acts with ROOT UV-B SENSITIVE1 in a Root Ultraviolet B-Sensing Pathway
Plant Physiology, August 1, 2009; 150(4): 1902 - 1915.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
D. Volodarsky, N. Leviatan, A. Otcheretianski, and R. Fluhr
HORMONOMETER: A Tool for Discerning Transcript Signatures of Hormone Action in the Arabidopsis Transcriptome
Plant Physiology, August 1, 2009; 150(4): 1796 - 1805.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
S.-Y. Jiang, A. Christoffels, R. Ramamoorthy, and S. Ramachandran
Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome
Plant Physiology, August 1, 2009; 150(4): 1997 - 2008.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Yoshida, Y. Makita, N. Heida, S. Asano, A. Matsushima, M. Ishii, Y. Mochizuki, H. Masuya, S. Wakana, N. Kobayashi, et al.
PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W147 - W152.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
T. Kuromori, S. Takahashi, Y. Kondou, K. Shinozaki, and M. Matsui
Phenome Analysis in Plant Species Using Loss-of-Function and Gain-of-Function Mutants
Plant Cell Physiol., July 1, 2009; 50(7): 1215 - 1231.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Krallinger, C. Rodriguez-Penagos, A. Tendulkar, and A. Valencia
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W160 - W165.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
Y. Makita, N. Kobayashi, Y. Mochizuki, Y. Yoshida, S. Asano, N. Heida, M. Deshpande, R. Bhatia, A. Matsushima, M. Ishii, et al.
PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants
Plant Cell Physiol., July 1, 2009; 50(7): 1249 - 1259.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
K. Iida, K. Fukami-Kobayashi, A. Toyoda, Y. Sakaki, M. Kobayashi, M. Seki, and K. Shinozaki
Analysis of Multiple Occurrences of Alternative Splicing Events in Arabidopsis thaliana Using Novel Sequenced Full-Length cDNAs
DNA Res, June 1, 2009; 16(3): 155 - 164.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
K. Vandepoele, M. Quimbaya, T. Casneuf, L. De Veylder, and Y. Van de Peer
Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks
Plant Physiology, June 1, 2009; 150(2): 535 - 546.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. D. Lehti-Shiu, C. Zou, K. Hanada, and S.-H. Shiu
Evolutionary History and Stress Regulation of Plant Receptor-Like Kinase/Pelle Genes
Plant Physiology, May 1, 2009; 150(1): 12 - 26.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
S. M. Brady and N. J. Provart
Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology
PLANT CELL, April 1, 2009; 21(4): 1034 - 1051.
[Abstract] [Full Text] [PDF]

Home page
 J R Soc InterfaceHome page
G. A Reeves, D. Talavera, and J. M Thornton
Genome and proteome annotation: organization, interpretation and integration
J R Soc Interface, February 6, 2009; 6(31): 129 - 147.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
K. A. Howell, R. Narsai, A. Carroll, A. Ivanova, M. Lohse, B. Usadel, A. H. Millar, and J. Whelan
Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process
Plant Physiology, February 1, 2009; 149(2): 961 - 980.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
Y. Ogata, N. Sakurai, K. Aoki, H. Suzuki, K. Okazaki, K. Saito, and D. Shibata
KAGIANA: An Excel-Based Tool for Retrieving Summary Information on Arabidopsis Genes
Plant Cell Physiol., January 1, 2009; 50(1): 173 - 177.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
Y. Wamboldt, S. Mohammed, C. Elowsky, C. Wittgren, W. B.M. de Paula, and S. A. Mackenzie
Participation of Leaky Ribosome Scanning in Protein Dual Targeting by Alternative Translation Initiation in Higher Plants
PLANT CELL, January 1, 2009; 21(1): 157 - 167.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. M. Riano-Pachon, A. Nagel, J. Neigenfind, R. Wagner, R. Basekow, E. Weber, B. Mueller-Roeber, S. Diehl, and B. Kersten
GabiPD: the GABI primary database--a plant integrative 'omics' database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D954 - D959.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
The UniProt Consortium
The Universal Protein Resource (UniProt) 2009
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D169 - D174.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Bulow, S. Engelmann, M. Schindler, and R. Hehl
AthaMap, integrating transcriptional and post-transcriptional data
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D983 - D986.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Obayashi, S. Hayashi, M. Saeki, H. Ohta, and K. Kinoshita
ATTED-II provides coexpressed gene networks for Arabidopsis
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D987 - D991.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z.-y. Peng, X. Zhou, L. Li, X. Yu, H. Li, Z. Jiang, G. Cao, M. Bai, X. Wang, C. Jiang, et al.
Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D975 - D982.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Wilson, R. Pethica, Y. Zhou, C. Talbot, C. Vogel, M. Madera, C. Chothia, and J. Gough
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D380 - D386.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Choudhury and A. Lahiri
Arabidopsis thaliana regulatory element analyzer
Bioinformatics, October 1, 2008; 24(19): 2263 - 2264.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
A. Brautigam, S. Hoffmann-Benning, and A. P.M. Weber
Comparative Proteomics of Chloroplast Envelopes from C3 and C4 Plants Reveals Specific Adaptations of the Plastid Envelope to C4 Photosynthesis and Candidate Proteins Required for Maintaining C4 Metabolite Fluxes
Plant Physiology, September 1, 2008; 148(1): 568 - 579.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
N. Menda, R. M. Buels, I. Tecle, and L. A. Mueller
A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes
Plant Physiology, August 1, 2008; 147(4): 1788 - 1799.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. G. Cote, P. Jones, L. Martens, R. Apweiler, and H. Hermjakob
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W372 - W376.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
D. K. Owens, A. B. Alerding, K. C. Crosby, A. B. Bandara, J. H. Westwood, and B. S.J. Winkel
Functional Analysis of a Predicted Flavonol Synthase Gene Family in Arabidopsis
Plant Physiology, July 1, 2008; 147(3): 1046 - 1061.
[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.