Annotation of plant gene function via combined genomics, metabolomics and informatics

Journal of Visualized Experiments

Volumn , Issue 64, 2012, Pages

  Tohge, Takayuki ^a   Fernie, Alisdair R ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

Bioinformatics; Computational biology; Functional annotation; Genetics; Issue 64; Metabolomics; Plant biology; Plant metabolism; Spectroscopy and structural analysis; Theoretical biology; Transcriptome analysis

Indexed keywords

ARTICLE; BIOLOGY; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; METABOLISM; METABOLOMICS; METHODOLOGY; MOLECULAR GENETICS; PLANT; PLANT GENE; PLANT GENOME;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; GENOMICS; METABOLOMICS; MOLECULAR SEQUENCE ANNOTATION; PLANTS;

EID: 84863768165     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/3487     Document Type: Article

References (16)

1. Aharoni, A., Keizer, L.C.P., Bouwmeester, H.J., Sun, Z.K., Alvarez-Huerta, M., Verhoeven, H.A., Blaas, J., van Houwelingen, A., De Vos, R.C.H., van der Voet, H., Jansen, R.C., Guis, M., Mol, J., Davis, R.W., Schena, M., van Tunen, A.J., & O'Connell, A.P. Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. Plant Cell. 12 647-661 (2000).
2. Akiyama, K., Chikayama, E., Yuasa, H., Shimada, Y., Tohge, T., Shinozaki, K., Hirai, M.Y., Sakurai, T., Kikuchi, J., & Saito, K. PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol. 8, 339-345 (2008).
3. Araujo, W.L., Ishizaki, K., Nunes-Nesi, A., Larson, T.R., Tohge, T., Krahnert, I., Witt, S., Obata, T., Schauer, N., Graham, I.A., Leaver, C.J., & Fernie, A.R. Identification of the 2-Hydroxyglutarate and Isovaleryl-CoA Dehydrogenases as Alternative Electron Donors Linking Lysine Catabolism to the Electron Transport Chain of Arabidopsis Mitochondria. Plant Cell. 22, 1549-1563 (2010).
4. De Vos, R.C.H., Moco, S., Lommen, A., Keurentjes, J.J.B., Bino, R.J., & Hall, R.D. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat. Protoc. 2 (2007).
5. Hirai, M.Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., Araki, R., Sakurai, N., Suzuki, H., Aoki, K., Goda, H., Nishizawa, O.I., Shibata, D., & Saito, K. Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 104, 6478-6483 (2007.
6. Mutwil, M., Klie, S., Tohge, T., Giorgi, F.M., Wilkins, O., Campbell, M.M., Fernie, A.R., Usadel, B., Nikoloski, Z., & Persson, S. Pla Net: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species. Plant Cell. 23, 895-910 (2011).
7. Mutwil, M., Ruprecht, C., Giorgi, F.M., Bringmann, M., Usadel, B., & Persson, S. Transcriptional Wiring of Cell Wall-Related Genes in Arabidopsis. Molecular Plant. 2, 1015-1024 (2009).
8. Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M., Shibata, D., Saito, K., & Ohta, H. ATTED-II: a database of co expressedgenes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Research. 35, D863-D869 (2007).
9. Ogata, Y., Suzuki, H., Sakurai, N., & Shibata, D. CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics. 26, 1267-1268 (2010).
10. Persson, S., Wei, H.R., Milne, J., Page, G.P., & Somerville, C.R. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proceedings of the National Academy of Sciences of the United States of America. 102, 8633-8638 (2005).
11. Tohge, T., Yonekura-Sakakibara, K., Niida, R., Watanabe-Takahashi, A., & Saito, K. Phytochemical genomics in Arabidopsis thaliana: A case study for functional identification of flavonoid biosynthesis genes. Pure and Applied Chemistry. 79, 811-823 (2007).
12. Tohge, T. & Fernie, A.R. Web-based resources for mass-spectrometry-based metabolomics: A user's guide. Phytochemistry. 70, 450-456 (2009).
13. Tohge, T. & Fernie, A.R. Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nature Protocols. 5, 1210-1227 (2010).
14. Tohge, T., Kusano, M., Fukushima, A., Saito, K., & Fernie, A.R. Transcriptional and metabolic programs following exposure of plants to UV-B irradiation. Plant Signal Behav. 6, In Press, (2011).
15. Tohge, T., Ramos, M.S., Nunes-Nesi, A., Mutwil, M., Giavalisco, P., Steinhauser, D., Schellenberg, M., Willmitzer, L., Persson, S., Martinoia, E., & Fernie, A.R. Towards the storage metabolome: profiling the barley vacuole. Plant Physiol. Epub ahead of print, PMID: 21949213 (2011).
16. Yonekura-Sakakibara, K., Tohge, T., Matsuda, F., Nakabayashi, R., Takayama, H., Niida, R., Watanabe-Takahashi, A., Inoue, E., & Saito, K. Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. Plant Cell. 20, 2160-2176 (2008).