ゲノムネットワークプロジェクト

ヒトゲノムネットワークプラットフォーム構築
研究課題 蛋白質相互作用の変化を推定するアルゴリズムの開発
研究期間 平成16年度〜20年度
研究課題代表者 郷 通子
所属機関 長浜バイオ大学バイオサイエンス学部
公開システム AS-ALPS
研究目的 ヒトゲノムの半数以上の遺伝子からスプライシングバリアントの発現が観察されている。蛋白質相互作用の多様化を通した蛋白質ネットワークへの寄与という観点から、選択的スプライシング(AS)の役割を推定する。
研究概要 蛋白質立体構造情報を駆使し、ASがどのように蛋白質立体構造に影響を与え、その結果、蛋白質相互作用にどのような変化を及ぼすかを推定するアルゴリズムを開発した。
研究成果 開発したアルゴリズムを用いて網羅的解析を行った結果、ヒトおよびマウスの大多数のASが、蛋白>質ドメインの安定性や相互作用部位に直接影響を与え、蛋白質相互作用を変化させると推定された。また、解析結果をデータベースAS-ALPS(Alternative Splicing-induced ALteration of Protein Structure)としてインターネット上に公開した。立体構造情報から抽出した相互作用部位情報を基に、ASが相互作用に与える影響を直接的に推定できるのは、世界で公開されているASデータベースの中で唯一AS-ALPSだけである。
データ種別 -
対象生物 ヒト、マウス
組織・細胞株 -
対象遺伝子 -
実験情報 -
産出データ
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研究論文・特許出願・
学術発表など
------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1024
PUBLICATION TYPE: Conference
PUBLICATION NAME: 第76回日本遺伝学会大会
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2004-09-28
TITLE: 選択的スプライシングが及ぼすタンパク質構造・機能への影響
STATUS: Presented
AUTHOR NAME: 塩生真史1、由良敬2、伊藤剛3,4、今西規4、五條堀孝4,5、郷通子6
AUTHOR AFFILIATION: 1横浜市立大・院総合理・生体超分子、2原研・計算科学セ・量子生命、3農業生物資源研・ゲノム、4産総研・BIRC、5遺伝研・DDBJ、6長浜バイオ大・バイオサイエンス

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1025
PUBLICATION TYPE: Conference
PUBLICATION NAME: Symposium on Alternate Transcript Diversity
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2004-11-22
TITLE: Development of a method for assessing the influence of alternative splicing based on protein three-dimensional structure
STATUS: Presented
AUTHOR NAME: Masafumi Shionyu1, Kei Yura2, Kazuki Shinoda3, Ken-ichi Takahashi4 and Mitiko Go4
AUTHOR AFFILIATION: 1Dept. Sci. Biol. Supramol. Sys., Grad. Sch. Int. Sci., Yokohama City Univ., 2Quantum Bioinform., Cent. Prom. Comp. Sci. Eng., JAERI, 3Div. Bio. Sci., Grad. Sch. Sch., Nagoya Univ., 4Dept. Bio-Sci., Nagahama Inst. Bio-Sci. Tech.

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1026
PUBLICATION TYPE: Conference
PUBLICATION NAME: 生物物理学会第42回年会
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2004-12-15
TITLE: 選択的スプライシングによる蛋白質立体構造への影響
STATUS: Presented
AUTHOR NAME: 塩生真史1、由良敬2、萩野圭3、土方敦司3、平島義紀3、中原拓3、江口達也3、篠田和紀3、山口晶大4、高橋健一4、伊藤剛5,6、今西規6、五條堀孝6,7、郷通子4
AUTHOR AFFILIATION: 1横浜市立大・院総合理・生体超分子、2原研・計算科学セ・量子生命、3名大・院理・生命理学、4長浜バイオ大・バイオサイエンス、5農業生物資源研・ゲノム、6産総研・BIRC、7遺伝研・DDBJ

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1027
PUBLICATION TYPE: Conference
PUBLICATION NAME: 生物物理学会第43回年会
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2005-11-24
TITLE: 選択的スプライシングによるタンパク質多様化
STATUS: Presented
AUTHOR NAME: 塩生真史1, 由良敬2, 土方敦司3, 中原拓3, 篠田和紀3, 山口晶大1, 高橋健一1, 郷通子1,4
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------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1028
PUBLICATION TYPE: Conference
PUBLICATION NAME: IUBMB Internal Congress of Biochemistry and Molecular Biology
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2006-06-22
TITLE: Systematic detection of protein regions affected by alternative splicing
STATUS: Presented
AUTHOR NAME: Masafumi Shionyu 1, Kei Yura 2, Atsushi Hijikata 3, Taku Nakahara 3, Kazuki Shinoda 3, Akihiro Yamaguchi 1, Ken-ichi Takahashi 1, Mitiko Go 1,4
AUTHOR AFFILIATION: 1: Fac. Bio-Sci., Nagahama Inst. Bio-Sci. Tech., 2: Quantum Bioinfo., JAEA, 3: Grad. Sch. Sci., Nagoya Univ., 4: Ochanomizu Univ.

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1029
PUBLICATION TYPE: Conference
PUBLICATION NAME: EABS&BSJ 2006
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2006-11-13
TITLE: A possible effect of alternative splicing on multiple regions of a single protein
STATUS: Presented
AUTHOR NAME: Masafumi Shionyu1, Kei Yura2, Mitiko Go1, 3
AUTHOR AFFILIATION: 1Fac. Bio-Sci., Nagahama Inst. Bio-Sci. Tech. 2Quantum Bioinfo., JAEA 3Ochanomizu Univ.

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1030
PUBLICATION TYPE: Conference
PUBLICATION NAME: International Symposium on Frontiers of Computational Science 2005
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2005-12-13
TITLE: Contribution of Computational Biology and Structural Genomics
STATUS: Presented
AUTHOR NAME: Mitiko Go
AUTHOR AFFILIATION: 1Fac. Bio-Sci., Nagahama Inst. Bio-Sci. Tech., 2Ochanomizu Univ.

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1031
PUBLICATION TYPE: Conference
PUBLICATION NAME: EABS&BSJ 2006
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2006-11-12
TITLE: Computational Biology to Understand Genome and Transcriptome
STATUS: Presented
AUTHOR NAME: Mitiko Go
AUTHOR AFFILIATION: 1Fac. Bio-Sci., Nagahama Inst. Bio-Sci. Tech., 2Ochanomizu Univ.

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1032
PUBLICATION TYPE: Conference
PUBLICATION NAME: 第9回日本進化学会大会
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2007-09-02
TITLE: 真核生物の遺伝子構造とタンパク質立体構造・機能の関係
STATUS: Presented
AUTHOR NAME: 由良敬1、塩生真史2、郷通子2,3
AUTHOR AFFILIATION: 1原子力機構・量子生命、2長浜バイオ大・バイオサイエンス、3お茶の水女子大学

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1033
PUBLICATION TYPE: Conference
PUBLICATION NAME: 生物物理学会第45回年会
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2007-12-21
TITLE: Alternative Splicing and Its Influence on Protein Conformation
STATUS: Presented
AUTHOR NAME: Mitiko Go1,2, Kei Yura3,4, Masafumi Shionyu2
AUTHOR AFFILIATION: 1: Ochanomizu Univ.; 2: Dept. of Bio-Science, Nagahama Inst. of Bio-Science and Technology; 3: Quantum Bioinf., JAEA; 4 Res. Unit Quantum Beam Life Sci., JAEA

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1275
PUBLICATION TYPE: journal
PUBLICATION NAME: Mol. Biol. Evol.
ARTICLE TITLE: Alternative splicing at NAGNAG acceptor sites shares common properties in land plants and mammals
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2008-01-29
TITLE: Alternative splicing at NAGNAG acceptor sites shares common properties in land plants and mammals
STATUS: Published
AUTHOR NAME: Iida K, Shionyu M, Suso Y
AUTHOR AFFILIATION: Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1524
PUBLICATION TYPE: Conference
PUBLICATION NAME: The Thirteenth "Science in Japan" Forum
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2008-06-20
TITLE: Information Flow from DNA Sequence to Protein Function
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AUTHOR NAME: Kei Yura1, Mitiko Go1,2
AUTHOR AFFILIATION: 1: Ochanomizu University, 2: Nagahama Institute of Bio-Science and Technology

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1613
PUBLICATION TYPE: Conference
PUBLICATION NAME: 日本遺伝学会第80回大会
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2008-09-03
TITLE: Construction of a database to infer alternative splicing-induced diversification of protein structure and interaction
STATUS: Presented
AUTHOR NAME: Masafumi Shionyu1, Akihiro Yamaguchi1, Ken-ichi Takahashi1, Mitiko Go1,2
AUTHOR AFFILIATION: 1:Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology; 2:Ochanomizu University

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1614
PUBLICATION TYPE: Conference
PUBLICATION NAME: 第31回日本分子生物学会年会
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2008-12-12
TITLE: 選択的スプライシングの影響を蛋白質立体構造に基づき推定するためのデータベースの構築
STATUS: Presented
AUTHOR NAME: 塩生真史1、山口晶大1、高橋健一1、郷通子1,2,3
AUTHOR AFFILIATION: 1:長浜バイオ大学バイオサイエンス学部、2:お茶の水女子大学、3:東京医科歯科大学

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1615
PUBLICATION TYPE: journal
PUBLICATION NAME: Nucleic Acids Research 2009 37(Database issue):D305-D309
ARTICLE TITLE: AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse
SUBMIT DATE: 2008-08-11
ACCEPT DATE: 2008-10-18
PUBLICATION DATE: 2008-11-10
TITLE: AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse
STATUS: Published
AUTHOR NAME: Masafumi Shionyu,1 Akihiro Yamaguchi,1 Kazuki Shinoda,1 Ken-ichi Takahashi,1 and Mitiko Go1,2,3
AUTHOR AFFILIATION: 1:Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology; 2:Ochanomizu University; 3:Tokyo Medical and Dental University

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1849
PUBLICATION TYPE: journal
PUBLICATION NAME: in preparation
ARTICLE TITLE: A systematic method for assessing the influence of alternative splicing events on protein interaction sites
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE:
TITLE: A systematic method for assessing the influence of alternative splicing events on protein interaction sites
STATUS: Preparation
AUTHOR NAME: Masafumi Shionyu1, Ken-ichi Takahashi1, Kazuki Shinoda1, Mitiko Go1, 2, 3
AUTHOR AFFILIATION: 1 Department of Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266, Tamura-cho, Nagahama, Shiga 526-0829, Japan 2 Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan 3 Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1878
PUBLICATION TYPE: Conference
PUBLICATION NAME: 第5回日本バイオインフォマティクス学会九州支部講演会・第5回グローバルCOE技術習得コース「バイオインフォマティクスの最近のトピックス」
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2009-02-27
TITLE: 選択的スプライシングがタンパク質立体構造・機能に与える影響の解析
STATUS: Presented
AUTHOR NAME: 塩生真史
AUTHOR AFFILIATION: 長浜バイオ大学・バイオサイエンス学部

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