KaPPA-View. A Web-Based Analysis Tool for Integration of Transcript and Metabolite Data on Plant Metabolic Pathway Maps
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- Toshiaki Tokimatsu
- 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, Send
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- Nozomu Sakurai
- 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, Send
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- Hideyuki Suzuki
- 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, Send
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- Hiroyuki Ohta
- 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, Send
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- Kazuhiko Nishitani
- 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, Send
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- Tanetoshi Koyama
- 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, Send
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- Toshiaki Umezawa
- 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, Send
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- Norihiko Misawa
- 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, Send
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- Kazuki Saito
- 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, Send
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- Daisuke Shibata
- 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, Send
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説明
<jats:title>Abstract</jats:title> <jats:p>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.</jats:p>
収録刊行物
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- Plant Physiology
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Plant Physiology 138 (3), 1289-1300, 2005-07-01
Oxford University Press (OUP)
