Construction of ATTED-III, Gene Coexpression Database for Arabidopsis

• Project/Area Number: 21770035
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Plant molecular biology/Plant physiology
• Research Institution: Tohoku University
• Principal Investigator: OBAYASHI Takeshi Tohoku University, 大学院・情報科学研究科, 助教 (50397048)
• Project Period (FY): 2009 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2010: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000); Fiscal Year 2009: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 環境応答 / バイオインフォマティクス / 遺伝子共発現 / シロイヌナズナ / マイクロアレイ / データベース

Research Abstract

ATTED-II, a coexpressed gene database for Arabidopsis, has been used to find functionally related gene groups. However, this traditional coexpression information cannot provide the detail of gene relationships. In this study, I constructed condition-specific coexpression data and two types of viewers to reveal the situation when and where the genes function together.

Research Products

• [Journal Article] Kinoshita K ATTED-II updates : condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. (2011)
  • Author(s): Obayashi T, Nishida K, Kasahara K
  • Journal Title: Plant Cell Physiol 52 Pages: 213-219
  • Peer Reviewed
• [Journal Article] COXPRESdb : a database to compare gene coexpression in seven model animals. (2011)
  • Author(s): Obayashi T, Kinoshita K
  • Journal Title: Nucleic Acids Res 39
  • Peer Reviewed
• [Journal Article] 共発現情報から見る遺伝子機能ネットワーク (2011)
  • Author(s): 大林武、木下賢吾
  • Journal Title: 化学と生物[KASEAA] 49 Pages: 48-56
  • NAID: 10027729287
• [Journal Article] ATTED-II updates : condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. (2011)
  • Author(s): Obayashi, et al.
  • Journal Title: Plant and Cell Physiology Volume: 52 Pages: 213-219
  • NAID: 10029708387
  • Peer Reviewed
• [Journal Article] COXPRESdb : a database to compare gene coexpression in seven model animals (2011)
  • Author(s): Obayashi, Kinoshita
  • Journal Title: Nucleic Acids Research Volume: 39 Pages: 1016-1022
  • Peer Reviewed
• [Journal Article] 共発現情報から見る遺伝子機能ネットワーク (2011)
  • Author(s): 大林武、木下賢吾
  • Journal Title: 化学と生物 Volume: 49 Pages: 48-66
  • NAID: 10027729287
• [Journal Article] Coexpression landscape in ATTED-II : usage of gene list and gene network for various types of pathways. (2010)
  • Author(s): Obayashi T, Kinoshita K
  • Journal Title: J. Plant Research 123 Pages: 311-319
  • NAID: 10027218882
  • Peer Reviewed
• [Journal Article] Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. (2009)
  • Author(s): Kinoshita K, Obayashi T
  • Journal Title: Bioinformatics 25 Pages: 2677-2684
  • Peer Reviewed
• [Journal Article] Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. (2009)
  • Author(s): Obayashi T, Kinoshita K
  • Journal Title: DNA Research 16 Pages: 249-260
  • Peer Reviewed
• [Journal Article] Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis (2009)
  • Author(s): Kinoshita, Obayashi
  • Journal Title: Bioinformatics 25 Pages: 2677-2684
  • Peer Reviewed
• [Journal Article] Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression (2009)
  • Author(s): Obayashi, Kinoshita
  • Journal Title: DNA Research 16 Pages: 249-260
  • Peer Reviewed
• [Journal Article] Coexpression landscape in ATTED-II : usage of gene list and gene network for various types of pathways
  • Author(s): Obayashi, Kinoshita
  • Journal Title: Journal of Plant Research (未定, 印刷中)
  • NAID: 10027218882
  • Peer Reviewed
• [Presentation] ATTED-II ver6:遺伝子共発現データの条件比較、種間比較 (2011)
  • Author(s): 大林武、木下賢吾
  • Organizer: 第52回日本植物生理学会年会
  • Place of Presentation: 東北大学
  • Year and Date: 2011-03-22
• [Presentation] How to measure the similarity of gene expression patterns to identify gene function (2011)
  • Author(s): Obayashi T
  • Organizer: QBIC2011 Bio-Informatics Workshop
  • Place of Presentation: 東京理科大学
  • Year and Date: 2011-03-11
• [Presentation] How to measure the similarity of gene expression patterns to identify gene function (2011)
  • Author(s): Takeshi Obayashi
  • Organizer: IC-QBIC2011 Bio-Informatics Workshop
  • Place of Presentation: Tokyo University of Science
  • Year and Date: 2011-03-11
• [Presentation] Rank of Correlation Coefficient Is a Comparable Measure of Gene Coexpression (2010)
  • Author(s): Obayashi T, Kinoshita K
  • Organizer: The 2010 Annual Conference of Japanese Society for Bioinformatics
  • Place of Presentation: 九州大学
  • Year and Date: 2010-12-13
• [Presentation] COXPRESdb : a gene coexpression database for 7 animal species (2010)
  • Author(s): Obayashi T, Kinoshita K
  • Organizer: 4th Asian Young Researchers Conference on Computational and Omics Biology
  • Place of Presentation: シンガポール、シンガポール共和国
  • Year and Date: 2010-12-01
• [Presentation] COXPRESdb : a gene coexpression database for 7 animal species (2010)
  • Author(s): Obayashi, Kinoshita
  • Organizer: The Asian Young Researchers Conference on Computational and Omics Biology 2010
  • Place of Presentation: Biopolis, Buona Vista, Singapore
  • Year and Date: 2010-12-01
• [Presentation] Number of microarray samples to construct effective gene coexpression data (2010)
  • Author(s): Obayashi T, Kinoshita K
  • Organizer: 第51回日本植物生理学会年会
  • Place of Presentation: 熊本大学
  • Year and Date: 2010-03-20
• [Presentation] Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression (2010)
  • Author(s): Takeshi Obayashi
  • Organizer: Asian Young Researchers Conference on Computational and Omics Biology 2010
  • Place of Presentation: National Cheng Kung University, Taiwan
  • Year and Date: 2010-03-11
• [Presentation] Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression (2010)
  • Author(s): Obayashi T, Kinoshita K
  • Organizer: Asian Young Researchers Conference on Computational and Omics Biology 2010
  • Place of Presentation: 台南、台湾
  • Year and Date: 2010-03-10
• [Presentation] Rank of Correlation Coefficient Is a Comparable Measure of Gene Coexpression (2010)
  • Author(s): Obayashi, Kinoshita
  • Organizer: The 2010 Annual Conference of Japanese Society for Bioinformatics (JSBi2010)
  • Place of Presentation: Centennial Hall Kyushu University School of Medicine
• [Presentation] COXPRESdb : A database of coexpressed gene networks for human, mouse and rat (2009)
  • Author(s): Obayashi T, Kinoshita K
  • Organizer: International congress of physiological sciences
  • Place of Presentation: 京都
  • Year and Date: 2009-07-27
• [Remarks]
  • URL: http://atted.jp
• [Remarks]
  • URL: http://atted.jp