This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Web of Science (32) Citing Articles via Google Scholar Google Scholar Articles by Tokimatsu, T. Articles by Shibata, D. Search for Related Content PubMed PubMed Citation Articles by Tokimatsu, T. Articles by Shibata, D. Agricola Articles by Tokimatsu, T. Articles by Shibata, D.

Bioinformatics

KaPPA-View. A Web-Based Analysis Tool for Integration of Transcript and Metabolite Data on Plant Metabolic Pathway Maps^1,[w]

Kazusa DNA Research Institute, Kisarazu, Chiba 292–0818, Japan (T.T., N.S., H.S., K.S., D.S.); Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori, Yokohama 226–8501, Japan (H.O.); Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980–8578, Japan (K.N.); Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba, Sendai 980–8577, Japan (T.K.); Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611–0011, Japan (T.U.); Marine Biotechnology Institute, Kamaishi, Iwate 026–0001, Japan (N.M.); and Graduate School of Pharmaceutical Sciences, Chiba University, Inage, Chiba 263–8522, Japan (K.S.)

The application of DNA array technology and chromatographic separation techniques coupled with mass spectrometry to transcriptomic and metabolomic analyses in plants has resulted in the generation of considerable quantitative data related to transcription and metabolism. The integration of "omic" data is one of the major concerns associated with research into identifying gene function. Thus, we developed a Web-based tool, KaPPA-View, for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. We prepared a set of comprehensive metabolic pathway maps for Arabidopsis (Arabidopsis thaliana) and depicted these graphically in Scalable Vector Graphics format. Individual transcripts assigned to a reaction are represented symbolically together with the symbols of the reaction and metabolites on metabolic pathway maps. Using quantitative values for transcripts and/or metabolites submitted by the user as Comma Separated Value-formatted text through the Internet, the KaPPA-View server inserts colored symbols corresponding to a defined metabolic process at that site on the maps and returns them to the user's browser. The server also provides information on transcripts and metabolites in pop-up windows. To demonstrate the process, we describe the dataset obtained for transgenic plants that overexpress the PAP1 gene encoding a MYB transcription factor on metabolic pathway maps. The presentation of data in this manner is useful for viewing metabolic data in a way that facilitates the discussion of gene function.

² Present address: Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba, 277–8561, Japan.

^[w] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.060525.

^* Corresponding author; e-mail shibata{at}kazusa.or.jp; fax 81–438–52–3948.

Received February 6, 2005; returned for revision April 28, 2005; accepted April 28, 2005.

This article has been cited by other articles:

				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]

				S. Mano, T. Miwa, S.-i. Nishikawa, T. Mimura, and M. Nishimura The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research Nucleic Acids Res., January 11, 2008; 36(suppl_1): D929 - D937. [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]

				K. Aoki, Y. Ogata, and D. Shibata Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology Plant Cell Physiol., March 1, 2007; 48(3): 381 - 390. [Abstract] [Full Text] [PDF]

				T. Obayashi, K. Kinoshita, K. Nakai, M. Shibaoka, S. Hayashi, M. Saeki, D. Shibata, K. Saito, and H. Ohta ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis Nucleic Acids Res., January 12, 2007; 35(suppl_1): D863 - D869. [Abstract] [Full Text] [PDF]

				N. Mitsuda, A. Iwase, H. Yamamoto, M. Yoshida, M. Seki, K. Shinozaki, and M. Ohme-Takagi NAC Transcription Factors, NST1 and NST3, Are Key Regulators of the Formation of Secondary Walls in Woody Tissues of Arabidopsis PLANT CELL, January 1, 2007; 19(1): 270 - 280. [Abstract] [Full Text] [PDF]

				N. Mitsuda, M. Seki, K. Shinozaki, and M. Ohme-Takagi The NAC Transcription Factors NST1 and NST2 of Arabidopsis Regulate Secondary Wall Thickenings and Are Required for Anther Dehiscence PLANT CELL, November 1, 2005; 17(11): 2993 - 3006. [Abstract] [Full Text] [PDF]