Backbone Database for Understanding the Biological Systems

2009 Fiscal Year Final Research Report

• Project/Area Number: 17020005
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kyoto University
• Principal Investigator: KANEHISA Minoru Kyoto University, 化学研究所, 教授 (70183275)
• Co-Investigator(Kenkyū-buntansha): HATTORI Masahiro 京都大学, 化学研究所, 助教 (60372554) ; KATAYAMA Toshiaki 東京大学, 医科学研究所, 助教 (60396869)
• Project Period (FY): 2005 – 2009
• Keywords: ゲノム / プロテオーム / バイオインフォマティクス / パスウェイ・ネットワーク / ケミカルゲノム

Research Abstract

We have expanded KEGG, an integrated database resource for understanding higher-level systemic functions and utilities of the cell, the organism, and the ecosystem from genomic and metagenomic information. Specifically, we have developed the genome annotation methods to predict molecular networks from genome sequences for deciphering the biological systems and the chemical annotation methods to predict chemical reactions from chemical compound structures for uncovering microbial degradation pathways of environmental compounds and biosynthetic pathways of plant secondary metabolites.

Research Products

• [Journal Article] PathPred: an enzyme-catalyzed metabolic pathway prediction server. (2010)
  • Author(s): Moriya, Y., Shigemizu, D., Hattori, M., Tokimatsu, T., Kotera, M., Goto, S., Kanehisa, M.
  • Journal Title: Nucleic Acids Res. Epub 2010
  • Peer Reviewed
• [Journal Article] KEGG for representation and analysis of molecular networks involving diseases and drugs. (2010)
  • Author(s): Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., Hirakawa, M.
  • Journal Title: Nucleic Acids Res. 38 Pages: D355-D360
  • Peer Reviewed
• [Journal Article] E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. (2009)
  • Author(s): Yamanishi, Y., Hattori, M., Kotera, M., Goto, S., Kanehisa, M.
  • Journal Title: Bioinformatics 25 Pages: i79-i86
  • Peer Reviewed
• [Journal Article] Extraction and analysis of chemical modification patterns in drug development. (2009)
  • Author(s): Shigemizu, D., Araki, M., Okuda, S., Goto, S., Kanehisa, M.
  • Journal Title: J. Chem. Inf. Model. 49 Pages: 1122-1129
  • Peer Reviewed
• [Journal Article] Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. (2009)
  • Author(s): Hashimoto, K., Tokimatsu, T., Kawano, S., Yoshizawa, A.C., Okuda, S., Goto, S., Kanehisa, M.
  • Journal Title: Carbohydr. Res. 344 Pages: 881-887
  • Peer Reviewed
• [Journal Article] Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. (2008)
  • Author(s): Yamanishi, Y., Araki, M., Gutteridge, A., Honda, W., Kanehisa, M.
  • Journal Title: Bioinformatics 24 Pages: 232-240
  • Peer Reviewed
• [Journal Article] KEGG Atlas mapping for global analysis of metabolic pathways. (2008)
  • Author(s): Okuda, S., Yamada, T., Hamajima, M., Itoh, M., Katayama, T., Bork, P., Goto, S., Kanehisa, M.
  • Journal Title: Nucleic Acids Res. 36 Pages: W423-W426
  • Peer Reviewed
• [Journal Article] Systematic survey for novel types of prokaryotic retroelements based on gene neighborhood and protein architecture. (2008)
  • Author(s): Kojima, K.K., Kanehisa, M.
  • Journal Title: Mol. Biol. Evol. 25 Pages: 1395-1404
  • Peer Reviewed
• [Journal Article] KEGG for linking genomes to life and the environment. (2008)
  • Author(s): Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., Yamanishi, Y.
  • Journal Title: Nucleic Acids Res. 36 Pages: D480-D484
  • Peer Reviewed
• [Journal Article] The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes. (2008)
  • Author(s): Hashimoto, K., Yoshizawa, A.C., Okuda, S., Kuma, K., Goto, S., Kanehisa, M.
  • Journal Title: J. Lipid Res. 49 Pages: 183-191
  • Peer Reviewed
• [Journal Article] Identification of endocrine disruptor biodegradation by integration of structure-activity relationship with pathway analysis. (2007)
  • Author(s): Kadowaki, T., Wheelock, C.E., Adachi, T., Kudo, T., Okamoto, S., Tanaka, N., Tonomura, K., Tsujimoto, G., Mamitsuka, H., Goto, S., Kanehisa, M.
  • Journal Title: Environ. Sci. Technol. 41 Pages: 7997-8003
  • Peer Reviewed
• [Journal Article] Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach. (2007)
  • Author(s): Fujita, M., Mihara, H., Goto, S., Esaki, N., Kanehisa, M.
  • Journal Title: BMC Bioinformatics 8 Pages: 225
  • Peer Reviewed
• [Journal Article] Observing metabolic functions at the genome scale. (2007)
  • Author(s): er, J.C., de Daruvar, A., Kanehisa, M.
  • Journal Title: Genome Biol. 8 Pages: R123
  • Peer Reviewed
• [Journal Article] Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. (2007)
  • Author(s): Itoh, M., Nacher, J.C., Kuma, K.I., Goto, S., Kanehisa, M.
  • Journal Title: Genome Biol. 8 Pages: R121
  • Peer Reviewed
• [Journal Article] The commonality of protein interaction networks determined in Neurodegenerative disorders (NDDs). (2007)
  • Author(s): Limviphuvadh, V., Tanaka, S., Goto, S., Ueda, K., Kanehisa, M.
  • Journal Title: Bioinformatics 23 Pages: 2129-2138
  • Peer Reviewed
• [Journal Article] KAAS: an automatic genome annotation and pathway reconstruction server. (2007)
  • Author(s): Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A., Kanehisa, M.
  • Journal Title: Nucleic Acids Res. 35 Pages: W182-W185
  • Peer Reviewed
• [Journal Article] Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. (2007)
  • Author(s): Oh, M., Yamada, T., Hattori, M., Goto, S., Kanehisa, M.
  • Journal Title: J. Chem. Inf. Model. 47 Pages: 1702-1712
  • Peer Reviewed
• [Journal Article] Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. (2007)
  • Author(s): Minowa, Y., Araki, M., Kanehisa, M.
  • Journal Title: J. Mol. Biol. 368 Pages: 1500-1517
  • Peer Reviewed
• [Journal Article] Prediction of missing enzyme genes in bacterial metabolic network: a reconstruction of lysine degradation pathway of Pseudomonas aeruginosa. (2007)
  • Author(s): Yamanishi, Y., Mihara, H., Osaki, M., Muramatsu, H., Esaki, N., Sato, T., Hizukuri, Y., Goto, S., Kanehisa, M.
  • Journal Title: FEBS J. 274 Pages: 2262-2273
  • Peer Reviewed
• [Journal Article] Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis. (2007)
  • Author(s): Okamoto, S., Yamanishi, Y., Ehira, S., Kawashima, S., Tonomura, K., Kanehisa, M.
  • Journal Title: Proteomics 7 Pages: 900-909
  • Peer Reviewed
• [Journal Article] Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic. (2006)
  • Author(s): Yoshizawa, A.C., Kawashima, S., Okuda, S., Fujita, M., Itoh, M., Moriya, Y., Hattori, M., Kanehisa, M.
  • Journal Title: Traffic 7 Pages: 1104-1118
  • Peer Reviewed
• [Journal Article] EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. (2006)
  • Author(s): Masoudi-Nejad, A., Tonomura, K., Kawashima, S., Moriya, Y., Suzuki, M., Itoh, M., Kanehisa, M., Endo, T., Goto, S.
  • Journal Title: Nucleic Acids Res. 34 Pages: W459-W462
  • Peer Reviewed
• [Journal Article] KEGG as a glycome informatics resource. (2006)
  • Author(s): Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., Kawasaki, T., Kanehisa, M.
  • Journal Title: Glycobiology 16 Pages: 63R-70R
  • Peer Reviewed
• [Journal Article] Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. (2006)
  • Author(s): Schwartz, J.M., Kanehisa, M.
  • Journal Title: BMC Bioinformatics 7 Pages: 186
  • Peer Reviewed
• [Journal Article] Extraction of phylogenetic network modules from the metabolic network. (2006)
  • Author(s): Yamada, T., Kanehisa, M., Goto, S.
  • Journal Title: BMC Bioinformatics 7 Pages: 130
  • Peer Reviewed
• [Journal Article] From genomics to chemical genomics: new developments in KEGG. (2006)
  • Author(s): Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., Hirakawa, M.
  • Journal Title: Nucleic Acids Res. 34 Pages: D354-357
  • Peer Reviewed
• [Journal Article] A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. (2005)
  • Author(s): Schwartz, J.M., Kanehisa, M.
  • Journal Title: Bioinformatics 21 Pages: ii204-ii205
  • Peer Reviewed
• [Journal Article] Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. (2005)
  • Author(s): Kawano, S., Hashimoto, K., Miyama, T., Goto, S., Kanehisa, M.
  • Journal Title: Bioinformatics 21 Pages: 3976-3982
  • Peer Reviewed
• [Journal Article] Extraction of leukemia specific glycan motifs in human by computational glycomics. (2005)
  • Author(s): Hizukuri, Y., Yamanishi, Y., Nakamura, O., Yagi, F., Goto, S., Kanehisa, M.
  • Journal Title: Carbohydr. Res. 340 Pages: 2270-2278
  • Peer Reviewed
• [Presentation] From metagenomes to pathways and diseases. (2010)
  • Author(s): Kanehisa, M.
  • Organizer: First International Conference on Human Metagenomics
  • Place of Presentation: Shenzhen, China
  • Year and Date: 2010-03-03
• [Book] Knowledge based analysis of protein interaction networks in neurodegenerative diseases. In "Neuroproteomics" (Alzate, O., ed. ) (2009)
  • Author(s): Kanehisa, M., Limviphuvadh, V., Tanabe, M.
  • Total Pages: 147-162
  • Publisher: CRC Press
• [Remarks] Thompson社ScienceWatchのEmerging Research Frontsにインタビュー記事(2008年2月)
• [Remarks] GenomeWeb社のBioInformにインタビュー記事(2008年1月)
• [Remarks] Thompson社Fast Breaking Paperに採択されインタビュー記事(2007年2月)
• [Remarks] KEGGデータベース
  • URL: http://www.genome.jp/kegg/