Genome-level integration of gene functional information and its application to elucidation of gene systems

• Project/Area Number: 15011229
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Osaka University
• Principal Investigator: MATSUDA Hideo Osaka University, Graduate School of Information Science and Technology, Professor, 大学院情報科学研究科, 教授 (50183950)
• Co-Investigator(Kenkyū-buntansha): BONO Hidemasa Saitama Medical School, School of Medicine, Associate Professor, 医学部, 助教授 (20364789)
• Project Period (FY): 2003 – 2004
• Project Status: Completed (Fiscal Year 2004)
• Budget Amount: ¥32,000,000 (Direct Cost: ¥32,000,000); Fiscal Year 2004: ¥16,000,000 (Direct Cost: ¥16,000,000); Fiscal Year 2003: ¥16,000,000 (Direct Cost: ¥16,000,000)
• Keywords: Microarray / Metabolic Pathway / Transcription Factor / Transcription Factor Binding Site / Gene Regulatory Network / 遺伝子配列解析 / クラスタリング / DNAチップ / 配列モチーフ / ゲノム情報解析 / 機能注釈 / cDNA / モチーフ / 代謝パスウェイ

Research Abstract

Although a large amount of data about genes from the genomes of many organisms has been obtained, the filmdom of many genes are still uncharacterized. This was due to the facts that the information of gene functions were not systematically arranged and not easily utilized, and the method for classifying genes to the gene families of functionally-coupled groups with their sequence homologies or expression similarities. To cope with these issues, this study aims to elucidate gene systems focusing on gene interactions by developing methods for systematic extraction of clearly-characterized gene functions and systematic arrangement of the extracted functional information in genome level.
The achievements of this study are:
(1) More accurate inference of gene regulatory networks with Bayesian network from gene expression data by using the functional classification of Gene Ontology as well as expression similarity.
(2) Mapping genes on microarrays onto the KEGG metabolic pathway database, construction of the system for analyzing the genes with their microarray data, the computational analysis of the tryptophan degradation pathway in mouse and the prediction of the existence of an alternative pathway.
(3) Development of analysis pipeline called SayaMatcher for finding the transcription-factor binding sites of which number is expected as several thousands to several hundreds of thousands.
(4) Construction of a DAS (Distributed Annotation System) server that makes it possible to display and browse those found binding sites and their positions on the genome.

Research Products

• [Journal Article] SayaMatcher : genome scale organization and systematic analysis of nuclear receptor response elements (2005)
  • Author(s): Bono H
  • Journal Title: Gene 364 Pages: 74-78
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] The study of metabolic pathways in tumors based on the transcriptome (2005)
  • Author(s): Bono H
  • Journal Title: Seminars in Cancer Biology 15 Pages: 290-299
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] SayaMatcher : genome scale organization and systematic analysis of nuclear receptor response elements (2005)
  • Author(s): Bono, H.
  • Journal Title: Gene 364 Pages: 74-78
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The study of metabolic pathways in tumors based on the transcriptome (2005)
  • Author(s): Bono, H., Okazaki, Y.
  • Journal Title: Seminars in Cancer Biology 15(4) Pages: 290-299
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] MaXML : Mouse Annotation XML (2004)
  • Author(s): Kasukawa T
  • Journal Title: In Silico Biology 4 Pages: 7-15
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Graph-based Clustering for Finding Distant Relationships in a Large Set of Protein Sequences (2004)
  • Author(s): Kawaji H
  • Journal Title: Bioinformatics 20 Pages: 243-252
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Identification and functional analysis of consensus androgen response elements in human prostate cancer cells (2004)
  • Author(s): Horie-Inoue K
  • Journal Title: Biochem. Biophys. Res. Commun. 325 Pages: 1312-1317
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] 遺伝子の機能分類を利用した遺伝子制御ネットワーク推定手法 (2004)
  • Author(s): 瀧浩平
  • Journal Title: 情報科学技術レターズ 3 Pages: 23-24
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Biased Biological Functions of Horizontally Transferred Genes in Prokaryotic Genomes (2004)
  • Author(s): Nakamura Y
  • Journal Title: Nature Genetics 36 Pages: 760-766
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] MaXML : Mouse Annotation XML (2004)
  • Author(s): Kasukawa, T., Bono, H., Hayashizaki, Y., Okazaki, Y., Matsuda, H.
  • Journal Title: In Silico Biology 4(3) Pages: 7-15
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Graph-based Clustering for Finding Distant Relationships in a Large Set of Protein Sequences (2004)
  • Author(s): Kawaji, H., Takenaka, Y., Matsuda, H.
  • Journal Title: Bioinformatics 20(2) Pages: 243-252
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Identification and functional analysis of consensus androgen response elements in human prostate cancer cells. (2004)
  • Author(s): Horie-Inoue, K., Bono, H., Okazaki, Y., Inoue, S.
  • Journal Title: Biochem Biophys Res Commun. 325(4) Pages: 1312-1317
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Inference method of gene regulatory networks using gene functional classification (2004)
  • Author(s): Taki, K., Teramoto, R., Takenaka, Y., Matsuda, H.
  • Journal Title: Information Technology Letters 3 Pages: 23-24
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Biased Biological Functions of Horizontally Transferred Genes in Prokaryotic Genomes (2004)
  • Author(s): Nakamura, Y., Itoh, T., Matsuda, H., Gojobori, T.
  • Journal Title: Nature Genetics 36(7) Pages: 760-766
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Biased biological functions of horizontally transferred genes in prokarvotic genomes (2004)
  • Author(s): Y.Nakamura, T.I toh, H.Matsuda, T.Goiobori.
  • Journal Title: Nature Genetics 36・7 Pages: 760-766
• [Journal Article] 遺伝子の機能分類を利用した遺伝子制御ネットワーク推定手法 (2004)
  • Author(s): 瀧浩平, 寺本礼仁, 竹中要一, 松田秀雄
  • Journal Title: 情報科学技術レターズ 3 Pages: 23-24
• [Journal Article] Architecture of a Grid-Enabled Research Platform with Location-Transparency for Bioinformatics (2004)
  • Author(s): Y.Kido S.Date S.Takeda S.Hatano J.Ma S.Shimoio H.Matsuda
  • Journal Title: Genome Informatics l5・2 Pages: 3-12
  • NAID: 130003997344
• [Journal Article] A Method for Clustering Expression Data Based on Graph Structure (2004)
  • Author(s): S.Seno R.Teramoto Y.Takenaka, H.Matsuda
  • Journal Title: Genome Informatics 15・2 Pages: 151-160
• [Journal Article] Identification and functional analysis of consensus androgen response elements in human prostate cancer cells (2004)
  • Author(s): K.Horie-Inoue, H.Bono, Y.Okazaki, S.Inoue
  • Journal Title: Biochem Biophys Res Commun. 325・4 Pages: 1312-1317
• [Journal Article] Comprehensive analysis of the mouse metabolome based on the transcriptome (2003)
  • Author(s): Bono H
  • Journal Title: Genome Research 13 Pages: 1345-1349
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] A Clustering Method for Comparative Analysis between Genomes and Pathways (2003)
  • Author(s): Miyake S
  • Journal Title: 8th International Conference on Database Systems for Advanced Applications (DASFAA 2003) Pages: 327-334
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays (2003)
  • Author(s): Bono H
  • Journal Title: Genome Research 13 Pages: 1318-1323
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Mouse Proteome Analysis (2003)
  • Author(s): Kanapin A
  • Journal Title: Genome Research 13 Pages: 1335-1344
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] FANTOM-DB : マウスcDNA機能アノテーションデータベース (2003)
  • Author(s): 坊農秀雅
  • Journal Title: 生化学 75 Pages: 149-152
  • NAID: 10010528069
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] マイクロアレイ・DANチップデータを活用する (2003)
  • Author(s): 坊農秀雅
  • Journal Title: 蛋白質 核酸 酵素 48 Pages: 167-172
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Comprehensive analysis of the mouse metabolome based on the transcriptome. (2003)
  • Author(s): Bono, H., Nikaido, I., Kasukawa, T., Hayashizaki, Y., Okazaki, Y., RIKEN GER Group ; GSL Members
  • Journal Title: Genome Research 13(6b) Pages: 1345-1349
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A Clustering Method for Comparative Analysis between Genomes and Pathways (2003)
  • Author(s): Miyake, S., Tohsato, Y., Takenaka, Y., Matsuda, H.
  • Journal Title: 8th International Conference on Database Systems for Advanced Applications DASFAA2003 Pages: 327-334
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays (2003)
  • Author(s): Bono, H., Yagi, K., Kasukawa, T., Nikaido, I., Tominaga, N., Miki, R., Mizuno, Y., Tomaru, Y., Goto, Nitanda, H., Shimizu, D., Makino, H., Morita, T., Fujiyama, J., Sakai, T., Shimoji, T., Hume, D.A., Hayashizaki, Y., Okazaki, Y., RIKEN GER Group ; GSL Members
  • Journal Title: Genome Research 13(6b) Pages: 1318-1323
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Mouse Proteome Analysis (2003)
  • Author(s): Kanapin, A., Batalov, S., Davis, M.J., Gough, J., Grimmond, S., Kawaji, H., Magrane, M., Matsuda, H., Schoenbach, C., Teasdale, R.D., RIKEN GER Group, GSL Members, Yuan, Z.
  • Journal Title: Genome Research 13(6b) Pages: 1335-1344
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] FANTOM-DB : database of functional annotation of RIKEN mouse cDNA clones (2003)
  • Author(s): Bono H, Kasukawa T, Furuno M, Hayashizaki Y, Okazaki Y.
  • Journal Title: Seikagaku 75(2) Pages: 149-152
  • NAID: 10010528069
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Introduction to the practical analysis of DNA microarray data (2003)
  • Author(s): Bono H, Nakao MC.
  • Journal Title: Tanpakushitsu Kakusan Koso. 48(2) Pages: 167-172
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] READ : RIKEN Expression Array Database (2002)
  • Author(s): Bono H
  • Journal Title: Nucleic Acids Research 30 Pages: 211-213
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] FANTOM DB : database of Functional Annotation of RIKEN Mouse cDNA Clones (2002)
  • Author(s): Bono H
  • Journal Title: Nucleic Acids Research 30 Pages: 116-118
  • NAID: 10010528069
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Exploration of Novel Motifs derived from Mouse cDNA sequences (2002)
  • Author(s): Kawaji H
  • Journal Title: Genome Research 12 Pages: 367-378
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Functional transcriptomes : comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts (2002)
  • Author(s): Bono H
  • Journal Title: Current Opinion in Structural Biology 12 Pages: 355-361
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] READ : RIKEN Expression Array Database Nucleic (2002)
  • Author(s): Bono, H., Kasukawa, T., Hayashizaki, Y., Okazaki, Y.
  • Journal Title: Acids Research 30 Pages: 211-213
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] FANTOM DB : database of Functional Annotation of RIKEN Mouse cDNA Clones (2002)
  • Author(s): Bono, H., Kasukawa, T., Furuno, M., Hayashizaki, Y., Okazaki, Y.
  • Journal Title: Nucleic Acids Research 30 Pages: 116-118
  • NAID: 10010528069
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Exploration of Novel Motifs derived from Mouse cDNA sequences (2002)
  • Author(s): Kawaji, H., Schoenbach, C., Matsuo, Y., Kawai, J., Okazaki, Y., Hayashizaki, Y., Matsuda, H.
  • Journal Title: Genome Research 12(3) Pages: 367-378
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Functional transcriptomes comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts (2002)
  • Author(s): Bono, H., Okazaki Y.
  • Journal Title: Current Opinion in Structural Biology 12 Pages: 355-361
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] An Application of a Pathway Alignment Method to the Analysis of Metabolic Pathways (2001)
  • Author(s): Tohsato Y
  • Journal Title: Research Communications in Biochemistry, Cell and Molecular Biology 15 Pages: 179-191
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] An Application of a Pathway Alignment Method to the Analysis of Metabolic Pathways, Research Communications in Biochemistry (2001)
  • Author(s): Tohsato, Y., Matsuda, H, Hashimoto, A.
  • Journal Title: Cell and Molecular Biology 15(3/4) Pages: 179-191
  • Description: 「研究成果報告書概要(欧文)」より
• [Publications] H.Kawaji, et al.: "Graph-based clustering for finding distant relationships in a large set of protein sequences"Bioinformatics. 20・2. 243-252 (2004)
• [Publications] T.Kasukawa, et al.: "MaXML : mouse annotation XML"In Silico Biology. 4・3. (2003)
• [Publications] A.Kanapin, et al.: "Mouse Proteome Analysis"Genome Research. 13・6B. 1335-1344 (2003)
• [Publications] T.Kasukawa, et al.: "Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System"Genome Research. 13・6B. 1542-1551 (2003)
• [Publications] H.Bono, et al.: "Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays"Genome Research. 13・6B. 1318-1323 (2003)
• [Publications] H.Bono, et al.: "Comprehensive analysis of the mouse metabolome based on the transcriptome"Genome Research. 13・6B. 1345-1349 (2003)