Nucleic Acids Research Advance Access originally published online on November 27, 2006
Nucleic Acids Research 2007 35(Database issue):D863-D869; doi:10.1093/nar/gkl783
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2007, Vol. 35, Database issue D863-D869
© 2006 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.
Articles |
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
1 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan 2 Graduate School of Pharmaceutical Sciences, Chiba University Chiba 263-8522, Japan 3 Core Research for Evolutional Science and Technology, Japan Science and Technology Agency 4-1-8, Saitama 332-0012, Japan 4 Human Genome Center, Institute of Medical Science, The University of Tokyo 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan 5 Structure and Function of Biomolecules, SORST JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan 6 Graduate School of Information Science and Engineering, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan 7 Kazusa DNA Research Institute, Kisarazu Chiba 292-0812, Japan 8 RIKEN Plant Science Center, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama 230-0045, Japan 9 Research Center for the Evolving Earth and Planets, 4259-B-14 Nagatsuta-cho Midori-ku, Yokohama 226-8501, Japan
*To whom correspondence should be addressed at Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan. Tel: +81 45 924 5736; Fax: +81 45 924 5823; Email: atted{at}bio.titech.ac.jp
Received August 15, 2006. Revised September 25, 2006. Accepted September 29, 2006.
Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction database (ATTED-II) that provides co-regulated gene relationships based on co-expressed genes deduced from microarray data and the predicted cis elements. ATTED-II (http://www.atted.bio.titech.ac.jp) includes the following features: (i) lists and networks of co-expressed genes calculated from 58 publicly available experimental series, which are composed of 1388 GeneChip data in A.thaliana; (ii) prediction of cis-regulatory elements in the 200 bp region upstream of the transcription start site to predict co-regulated genes amongst the co-expressed genes; and (iii) visual representation of expression patterns for individual genes. ATTED-II can thus help researchers to clarify the function and regulation of particular genes and gene networks.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Lysenko, M. M. Hindle, J. Taubert, M. Saqi, and C. J. Rawlings Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases Brief Bioinform, November 1, 2009; 10(6): 676 - 693. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
 |
|
 A. Karve and B. d. Moore Function of Arabidopsis hexokinase-like1 as a negative regulator of plant growth J. Exp. Bot., October 1, 2009; 60(14): 4137 - 4149. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. A. Dobritsa, J. Shrestha, M. Morant, F. Pinot, M. Matsuno, R. Swanson, B. L. Moller, and D. Preuss CYP704B1 Is a Long-Chain Fatty Acid {omega}-Hydroxylase Essential for Sporopollenin Synthesis in Pollen of Arabidopsis Plant Physiology, October 1, 2009; 151(2): 574 - 589. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. E. Perez, J. S. Hoyer, A. I. Johnson, Z. R. Moody, J. Lopez, and N. J. Kaplinsky BOBBER1 Is a Noncanonical Arabidopsis Small Heat Shock Protein Required for Both Development and Thermotolerance Plant Physiology, September 1, 2009; 151(1): 241 - 252. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Jin, Z. Hong, W. Su, and J. Li From the Cover: A plant-specific calreticulin is a key retention factor for a defective brassinosteroid receptor in the endoplasmic reticulum PNAS, August 11, 2009; 106(32): 13612 - 13617. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Imamura, Y. Kanesaki, M. Ohnuma, T. Inouye, Y. Sekine, T. Fujiwara, T. Kuroiwa, and K. Tanaka R2R3-type MYB transcription factor, CmMYB1, is a central nitrogen assimilation regulator in Cyanidioschyzon merolae PNAS, July 28, 2009; 106(30): 12548 - 12553. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Sawada, A. Kuwahara, M. Nagano, T. Narisawa, A. Sakata, K. Saito, and M. Yokota Hirai Omics-Based Approaches to Methionine Side Chain Elongation in Arabidopsis: Characterization of the Genes Encoding Methylthioalkylmalate Isomerase and Methylthioalkylmalate Dehydrogenase Plant Cell Physiol., July 1, 2009; 50(7): 1181 - 1190. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Shinozaki and H. Sakakibara Omics and Bioinformatics: An Essential Toolbox for Systems Analyses of Plant Functions Beyond 2010 Plant Cell Physiol., July 1, 2009; 50(7): 1177 - 1180. [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 Y. Okazaki, M. Shimojima, Y. Sawada, K. Toyooka, T. Narisawa, K. Mochida, H. Tanaka, F. Matsuda, A. Hirai, M. Y. Hirai, et al. A Chloroplastic UDP-Glucose Pyrophosphorylase from Arabidopsis Is the Committed Enzyme for the First Step of Sulfolipid Biosynthesis PLANT CELL, March 1, 2009; 21(3): 892 - 909. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Bednarek, M. Pislewska-Bednarek, A. Svatos, B. Schneider, J. Doubsky, M. Mansurova, M. Humphry, C. Consonni, R. Panstruga, A. Sanchez-Vallet, et al. A Glucosinolate Metabolism Pathway in Living Plant Cells Mediates Broad-Spectrum Antifungal Defense Science, January 2, 2009; 323(5910): 101 - 106. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Sawada, K. Akiyama, A. Sakata, A. Kuwahara, H. Otsuki, T. Sakurai, K. Saito, and M. Y. Hirai Widely Targeted Metabolomics Based on Large-Scale MS/MS Data for Elucidating Metabolite Accumulation Patterns in Plants Plant Cell Physiol., January 1, 2009; 50(1): 37 - 47. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 A. Fukushima, M. Wada, S. Kanaya, and M. Arita SVD-based Anatomy of Gene Expressions for Correlation Analysis in Arabidopsis thaliana DNA Res, December 1, 2008; 15(6): 367 - 374. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Choudhury and A. Lahiri Arabidopsis thaliana regulatory element analyzer Bioinformatics, October 1, 2008; 24(19): 2263 - 2264. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Yamamoto, D. Maruyama, T. Endo, and S.-i. Nishikawa Arabidopsis thaliana Has a Set of J Proteins in the Endoplasmic Reticulum that are Conserved from Yeast to Animals and Plants Plant Cell Physiol., October 1, 2008; 49(10): 1547 - 1562. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kunieda, N. Mitsuda, M. Ohme-Takagi, S. Takeda, M. Aida, M. Tasaka, M. Kondo, M. Nishimura, and I. Hara-Nishimura NAC Family Proteins NARS1/NAC2 and NARS2/NAM in the Outer Integument Regulate Embryogenesis in Arabidopsis PLANT CELL, October 1, 2008; 20(10): 2631 - 2642. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Yamada, A. J. Nagano, M. Nishina, I. Hara-Nishimura, and M. Nishimura NAI2 Is an Endoplasmic Reticulum Body Component That Enables ER Body Formation in Arabidopsis thaliana PLANT CELL, September 1, 2008; 20(9): 2529 - 2540. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Yonekura-Sakakibara, T. Tohge, F. Matsuda, R. Nakabayashi, H. Takayama, R. Niida, A. Watanabe-Takahashi, E. Inoue, and K. Saito Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene-Metabolite Correlations in Arabidopsis PLANT CELL, August 1, 2008; 20(8): 2160 - 2176. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Krishnan and A. Pereira Integrative approaches for mining transcriptional regulatory programs in Arabidopsis Brief Funct Genomic Proteomic, July 16, 2008; (2008) eln035v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Wang, H. Wu, and M. Yang Microscopy and Bioinformatic Analyses of Lipid Metabolism Implicate a Sporophytic Signaling Network Supporting Pollen Development in Arabidopsis Mol Plant, July 1, 2008; 1(4): 667 - 674. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Srinivasasainagendra, G. P. Page, T. Mehta, I. Coulibaly, and A. E. Loraine CressExpress: A Tool For Large-Scale Mining of Expression Data from Arabidopsis Plant Physiology, July 1, 2008; 147(3): 1004 - 1016. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
A. Frelet-Barrand, H. U. Kolukisaoglu, S. Plaza, M. Ruffer, L. Azevedo, S. Hortensteiner, K. Marinova, B. Weder, B. Schulz, and M. Klein Comparative Mutant Analysis of Arabidopsis ABCC-Type ABC Transporters: AtMRP2 Contributes to Detoxification, Vacuolar Organic Anion Transport and Chlorophyll Degradation Plant Cell Physiol., April 1, 2008; 49(4): 557 - 569. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Wohlbach, B. F. Quirino, and M. R. Sussman Analysis of the Arabidopsis Histidine Kinase ATHK1 Reveals a Connection between Vegetative Osmotic Stress Sensing and Seed Maturation PLANT CELL, April 1, 2008; 20(4): 1101 - 1117. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Obayashi, S. Hayashi, M. Shibaoka, M. Saeki, H. Ohta, and K. Kinoshita COXPRESdb: a database of coexpressed gene networks in mammals Nucleic Acids Res., January 11, 2008; 36(suppl_1): D77 - D82. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Ma, Q. Gong, and H. J. Bohnert An Arabidopsis gene network based on the graphical Gaussian model Genome Res., November 1, 2007; 17(11): 1614 - 1625. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Ishihara, A. Takabayashi, K. Ido, T. Endo, K. Ifuku, and F. Sato Distinct Functions for the Two PsbP-Like Proteins PPL1 and PPL2 in the Chloroplast Thylakoid Lumen of Arabidopsis Plant Physiology, November 1, 2007; 145(3): 668 - 679. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Yonekura-Sakakibara, T. Tohge, R. Niida, and K. Saito Identification of a Flavonol 7-O-Rhamnosyltransferase Gene Determining Flavonoid Pattern in Arabidopsis by Transcriptome Coexpression Analysis and Reverse Genetics J. Biol. Chem., May 18, 2007; 282(20): 14932 - 14941. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Y. Hirai, K. Sugiyama, Y. Sawada, T. Tohge, T. Obayashi, A. Suzuki, R. Araki, N. Sakurai, H. Suzuki, K. Aoki, et al. Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis PNAS, April 10, 2007; 104(15): 6478 - 6483. [Abstract] [Full Text] [PDF]
|
|