KAGIANA: An excel-based tool for retrieving summary information on arabidopsis genes

Plant and Cell Physiology

Volumn 50, Issue 1, 2009, Pages 173-177

  Ogata, Yoshiyuki ^a   Sakurai, Nozomu ^a   Aoki, Koh ^a   Suzuki, Hideyuki ^a   Okazaki, Koei ^a   Saito, Kazuki ^b   Shibata, Daisuke ^a  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b CHIBA UNIVERSITY   (Japan)

Author keywords

Annotation; Arabidopsis; Database; Gene expression; Omics

Indexed keywords

ARABIDOPSIS; ARTICLE; BIOLOGY; DATA BASE; GENETIC DATABASE; GENETICS; PLANT GENE;

ARABIDOPSIS; COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENES, PLANT;

ARABIDOPSIS;

EID: 58449094078     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcn179     Document Type: Article

References (27)

1. Alonso, J.M., Stepanova, A.N., Leisse, T.J., Kim, C.J., Chen, H., Shinn, P., et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653-657.
2. Andreeva, A., Howorth, D., Chandonia, J.M., Brenner, S.E., Hubbard, T.J., Chothia, C., et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 36: D419-D425.
3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
4. Baerenfaller, K., Grossmann, J., Grobei, M.A., Hull, R., Hirsch-Hoffmann, M., Yalovsky, S., et al. (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320: 938-941.
5. Barrett, T., Troup, D.B., Willhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., et al. (2006) NCBI GEO: mining tens of millions of expression profiles - database and tools update. Nucleic Acids Res. 35: D760-D765.
6. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Wheeler, D.L. (2008) GenBank. Nucleic Acids Res 36: D25-D30.
7. Berglund, A.C., Sjölund, E., Östlund, G. and Sonnhammer, E.L. (2008) InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res. 36: D263-D266.
8. Brenner, S., Williams, S.R., Vermaas, E.H., Storck, T., Moon, K., McCollum, C., et al. (2000) In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc. Natl. Acad. Sci. USA 18: 630-634.
9. 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.
10. Emanuelsson, O., Brunak, S., von Heijne, G. and Nielsen, H. (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2: 953-971.
11. Gene Ontology Consortium (2008) The Gene Ontology project in 2008. Nucleic Acids Res. 36: D440-D444.
12. Gupta, A., Maranas, C.D. and Albert, R. (2006) Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites. Bioinformatics 22: 209-214.
13. Heazlewood, J.L., Verboom, R.E., Tonti-Filippini, J., Small, I. and Millar, A.H. (2007) SUBA: the Arabidopsis Subcellular Database. Nucleic Acids Res. 35: D213-D218.
14. Horton, P., Park, K.J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C.J., et al. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35: W585-W587.
15. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36: D480-D484.
16. Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E.S., Casstevens, T., et al. (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res. 36: D947-D953.
17. Maglott, D., Ostell, J., Pruitt, K.D. and Tatusova, T. (2005) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 33: D54-D58.
18. Margolin, A.A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Dalla-Favera, R., et al. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7: S7.
19. Möller, S., Croning, M.D.R. and Apweiler, R. (2001) Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17: 646-653.
20. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., et al. (2007) New developments in the InterPro database. Nucleic Acids Res 35: D224-D228.
21. 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.
22. Sakurai, N. and Shibata, D. (2006) KaPPA-View for integrating quantitative transcriptomic and metabolomic data on plant metabolic pathway maps. J. Pestic. Sci. 31: 293-295.
23. Sugawara, H., Ogasawara, O., Okubo, K., Gojobori, T. and Tateno, Y. (2008) DDBJ with new system and face. Nucleic Acids Res. 36: D22-D24.
24. 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.
25. Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G.V. and Provart, N.J. (2007) An 'electronic fluorescent pictograph' browser for exploring and analyzing large-scale biological data sets. PLoS ONE 2: e718.
26. Zhang, P., Foerster, H., Tissier, C.P., Mueller, L., Paley, S., Karp, P.D., et al. (2005) MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol. 138: 27-37.
27. Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L. and Gruissem, W. (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 136: 2621-2632.