ATTED-II updates: Condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants

Plant and Cell Physiology

Volumn 52, Issue 2, 2011, Pages 213-219

  Obayashi, Takeshi ^a   Nishida, Kozo ^b   Kasahara, Kota ^a   Kinoshita, Kengo ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Arabidopsis; Comparative transcriptomics; Database; Gene coexpression; Gene network; Rice

Indexed keywords

ARABIDOPSIS; ARTICLE; BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; METHODOLOGY; RICE;

ARABIDOPSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; ORYZA SATIVA;

ARABIDOPSIS; MAGNOLIOPHYTA;

EID: 79951562208     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcq203     Document Type: Article

References (24)

1. Aoki, K., Ogata, Y. and Shibata, D. (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol. 48: 381-390. (Pubitemid 47355543)
2. Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C. et al. (2007) NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res. 35: D760-D765. (Pubitemid 46056306)
3. Craigon, D.J., James, N., Okyere, J., Higgins, J., Jotham, J. and May, S. (2004) NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res. 32: D575-D577. (Pubitemid 38100464)
4. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95: 14863-14868. (Pubitemid 29003722)
5. Goda, H., Sasaki, E., Akiyama, K., Maruyama-Nakashita, A., Nakabayashi, K. et al. (2008) The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J. 55: 526-542. (Pubitemid 352033349)
6. Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O. et al. (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 50: 347-363. (Pubitemid 46624141)
7. Kinoshita, K. and Obayashi, T. (2009) Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. Bioinformatics 25: 2677-2684.
8. Lopes, C.T., Franz, M., Kazi, F., Donaldson, S.L., Morris, Q. and Bader, G.D. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26: 2347-2348.
9. Obayashi, T., Hayashi, S., Saeki, M., Ohta, H. and Kinoshita, K. (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res. 37: D987-D991.
10. Obayashi, T. and Kinoshita, K. (2009) Rank of correlation coefficient as a comparable measure for biological significance of gene coex-pression. DNA Res. 16: 249-260.
11. Obayashi, T. and Kinoshita, K. (2010) Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. J. Plant Res. 123: 311-319.
12. Obayashi, T. and Kinoshita, K. (2011) COXPRESdb: a database to compare gene coexpression in seven model animals. Nucleic Acids Res. (in press).
13. Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M. et al. (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res. 35: D863-D869. (Pubitemid 46056323)
14. Okazaki, Y., Shimojima, M., Sawada, Y., Toyooka, K., Narisawa, T., Mochida, K. et al. (2009) A chloroplastic UDP-glucose pyropho-sphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis. Plant Cell 21: 892-909.
15. Oti, M., van Reeuwijk, J., Huynen, M.A. and Brunner, H.G. (2008) Conserved co-expression for candidate disease gene prioritization. BMC Bioinformatics 9: 208.
16. Parkinson, H., Kapushesky, M., Kolesnikov, N., Rustici, G., Shojatalab, M., Abeygunawardea, N. et al. (2009) ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res. 37: D868-D872.
17. Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K. et al. (2010) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 38: D5-D16.
18. Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M. et al. (2005) A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37: 501-506. (Pubitemid 40617278)
19. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13: 2498-2504. (Pubitemid 37428274)
20. Steinhauser, D., Usadel, B., Luedemann, A., Thimm, O. and Kopka, J. (2004) CSB.DB: a comprehensive systems-biology database. Bioinformatics 20: 3647-3651. (Pubitemid 40136804)
21. Stuart, J.M., Segal, E., Koller, D. and Kim, S.K. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255. (Pubitemid 37248749)
22. Swarbreck, D., Wilks, C., Lamesch, P., Berardini, T.Z., Garcia-Hernandez, M., Foerster, H. et al. (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 36: D1009-D1014. (Pubitemid 351149860)
23. Toufighi, K., Brady, S.M., Austin, R., Ly, E. and Provart, N.J. (2005) The Botany Array Resource: e-Northerns, expression angling, and promoter analyses. Plant J. 43: 153-163. (Pubitemid 40962743)
24. Usadel, B., Obayashi, T., Mutwil, M., Giorgi, F.M., Bassel, G.W., Tanimoto, M. et al. (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ. 32: 1633-1651.