ゲノムネットワークプロジェクト

動的ネットワーク解析技術開発
研究課題 動的ネットワーク抽出のためのイン・シリコパイプラインの構成
研究期間 平成19年度〜20年度
研究課題代表者 宮野 悟
所属機関 東京大学医科学研究所
公開システム Human Genome Center
研究目的 マクロファージの分化・活性化ネットワークに関する遺伝子発現情報等の大規模・総合的データから動的転写制御ネットワークを抽出し、利用するための計算戦略をイン・シリコパイプラインとして構築する。
研究概要 状態空間モデルと次元圧縮技術により転写モジュールネットワーク構造を抽出し、さらに、複数ソース情報を利用した数理統計手法により転写制御ネットワーク構造を精緻化する方式を構築する。次に、データ同化技術により時系列データを利用してネットワーク構造へダイナミクスを導入する技術、及び文献キュレーション情報を用いて、動的な転写制御ネットワークを抽出するパイプラインを構築する。同時に、この動的転写制御ネットワークを開発・活用・発展させるためのソフトウェアプラットフォームを開発する。
研究成果 約 1000 万エントリーからなるヒトマクロファージデータベース及びそのための API ライブラリを開発した。状態空間モデルやデータ同化技術をはじめとする動的ネットワーク抽出技術は、 Cell Illustrator 環境で利用できるように JAVA コード化を完了し CSMLPipeline に統合をおこなった。 LPS 及び PMA 刺激に関連する文献キュレーションを行い、 CSML 形式の転写制御・シグナル伝達パスウェイモデルを約 80 個作成した。これらの動的モデルは、統合プラットフォーム "CelIllustrator Online for GNP" サーバのデータベース上で利用可能になっており、イン・シリコパイプライン構築を達成した。
データ種別 -
対象生物 -
組織・細胞株 -
対象遺伝子 -
実験情報 -
産出データ
(ダウンロード)
-
XMLデータ -
研究論文・特許出願・
学術発表など
------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1251
PUBLICATION TYPE: journal
PUBLICATION NAME: a
ARTICLE TITLE: Quality control and reproducibility in biological experiments
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2008-02-28
TITLE: Quality control and reproducibility in biological experiments (paper)
STATUS: Preparation
AUTHOR NAME: André Fujita1*, João Ricardo Sato2, Fernando Henrique Lojudice da Silva3, Maria Christina Galvão4, Mari Cleide Sogayar3, Satoru Miyano1
AUTHOR AFFILIATION: 1- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. 2- Institute of Mathematics and Statistics, University of São Paulo, Rua do Matão, 1010 - São Paulo, 05508-090, Brazil. 3- Chemistry Institute, University of São Paulo, Av. Lineu Prestes, 748 - São Paulo, 05513-970, Brazil. 4- Orthodontic Department, University Methodist of São Paulo, Rua Alfeu Tavares, 149 - São Bernardo do Campo, 09641-000, Brazil.

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1252
PUBLICATION TYPE: journal
PUBLICATION NAME: Journal of Bioinformatics and Computational Biology, 2009
ARTICLE TITLE: Comparing different methods for gene expression association analysis
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2008-02-28
TITLE: Comparing Pearson, Spearman and Hoeffding's D measure for gene expression association analysis.
STATUS: Accepted
AUTHOR NAME: Andre Fujita1, Joao Ricardo Sato2, Marcos Angelo Almeida Demasi3 , Mari Cleide Sogayar3, Carlos Eduardo Ferreira2 and Satoru Miyano1
AUTHOR AFFILIATION: 1Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan 2Institute of Mathematics and Statistics, University of Sao Paulo, Rua do Matao, 1010 - Sao Paulo, 05508-090, SP, Brazil 3Chemistry Institute, University of Sao Paulo, Av. Lineu Prestes, 748 - Sao Paulo, 05513-970, SP, Brazil

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1271
PUBLICATION TYPE: journal
PUBLICATION NAME: BMC Systems Biology, 2:106, 2008
ARTICLE TITLE: Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2008-03-31
TITLE: Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates
STATUS: Published
AUTHOR NAME: Andre Fujita1 Luciana Rogrigues Gomes2 Joao Ricardo Sato3 Rui Yamaguchi1 Carlos Eduardo Thomaz4 Mari Cleide Sogayar2 Satoru Miyano1
AUTHOR AFFILIATION: 1 - Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-4 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. 2 - Chemistry Institute, University of São Paulo, Av. Lineu Prestes, 748 - São Paulo, 05513-970, Brazil. 3 - Institute of Radiology, School of Medicine, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255 - São Paulo, 05403-001, Brazil. 4 - Department of Electrical Engineering, Centro Universitário da FEI, Av. Humberto de Alencar Castelo Branco, 3972 - São Bernardo do Campo, 09850-901, Brazil.

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1290
PUBLICATION TYPE: journal
PUBLICATION NAME: manuscript
ARTICLE TITLE: Inferring contagion in regulatory networks
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2008-04-25
TITLE: Inferring contagion in regulatory networks (paper)
STATUS: Submitted
AUTHOR NAME: Andre Fujita 1, Joao Ricardo Sato 2, Marcos Angelo Almeida Demasi 3, Rui Yamaguchi 1, Teppei Shimamura 1, Mari Cleide Sogayar 3 and Satoru Miyano 1
AUTHOR AFFILIATION: 1 Laboratory of DNA Information Analysis, Human Genome Center, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. 2 NIF-LIM44, Institute of Radiology, School of Medicine, University of Sao Paulo, Av. Dr. Eneas de Carvalho Aguiar, 255 - Sao Paulo, 05403-001, Brazil. 3 Cell and Molecular Biology Laboratory, Chemistry Institute, University of Sao Paulo, Av. Lineu Prestes, 748, Sao Paulo-SP, 05508-900, Brazil.

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1478
PUBLICATION TYPE: journal
PUBLICATION NAME: Journal of Bioinformatics and Computational Biology, 6:961-79, 2008
ARTICLE TITLE: Modeling nonlinear gene regulatory networks from time series gene expression data
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2007-12-01
TITLE: Modeling nonlinear gene regulatory networks from time series gene expression data
STATUS: Published
AUTHOR NAME: Andre Fujita1, Joao R. Sato2, Humberto M. Garay-Malpartida3, Mari Cleide Sogayar4, Carlos E. Ferreira2, Satoru Miyano1
AUTHOR AFFILIATION: 1 Human Genome Center, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan 2 Institute of Mathematics and Statistics, University of S˜ao Paulo, Rua do Mat˜ao,1010 Sao Paulo, SP, 05508-090, Brazil 3 Arts, Sciences and Humanities School, University of S˜ao Paulo, Av. Arlindo Bettio, 1000 Sao Paulo, SP, 03828-000, Brazil 4 Chemistry Institute, University of S˜ao Paulo, Av. Lineu Prestes, 748 Sao Paulo, SP, 05508-900, Brazil

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:1479
PUBLICATION TYPE: Book
PUBLICATION NAME: book chapter
ARTICLE TITLE: Dynamic Vector Autoregressive Model (DVAR)
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2008-06-06
TITLE: Dynamic Vector Autoregressive Model (DVAR) (Invited book chapter)
STATUS: Submitted
AUTHOR NAME: Andre Fujita1, Joao R. Sato2, Marcos A. Demasi3, Satoru Miyano1, Mari C. Sogayar3, Carlos E. Ferreira2
AUTHOR AFFILIATION: 1 Human Genome Center, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan 2 Institute of Mathematics and Statistics, University of S˜ao Paulo, Rua do Mat˜ao,1010 Sao Paulo, SP, 05508-090, Brazil 4 Chemistry Institute, University of Sao Paulo, Av. Lineu Prestes, 748 Sao Paulo, SP, 05508-900, Brazil

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:2003
PUBLICATION TYPE: Conference
PUBLICATION NAME: Pacific Symposium on Biocomputing
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2009-01-08
TITLE: A computational pipeline for gene expression data analysis and a comparative study between CAGE, illumina microarray and Quantitative Real Rime RT-PCR. (poster - Pacific Symposium on Biocomputing 2009)
STATUS: Presented
AUTHOR NAME: Andre Fujita1, Masao Nagasaki1, Seiya Imoto1, Ayumu Saito1, Emi Ikeda1, Teppei Shimamura1, Harukazu Suzuki1, Yoshihide Hayashizaki2, Satoru Miyano1.
AUTHOR AFFILIATION: 1- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan; 2-Genome LSA Technology Development Unit, Omics ScienceCenter, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:2004
PUBLICATION TYPE: Conference
PUBLICATION NAME: Asia Pacific Bioinformatics Conference
ARTICLE TITLE:
SUBMIT DATE:
ACCEPT DATE:
PUBLICATION DATE: 2008-01-16
TITLE: Modeling gene expression regulatory networks with the sparse vector autoregressive model (BMC Systems Biology, 2007 and poster Asia Pacific Bioinformatics Conference, 2008)
STATUS: Presented
AUTHOR NAME: Andre Fujita1, Joao Ricardo Sato2, Humberto Miguel Garay-Malpartida3, Rui Yamaguchi1, Mari Cleide Sogayar3, Carloes Eduardo Ferreira4, Satoru Miyano1
AUTHOR AFFILIATION: 1- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan; 2-Center of Mathematics, Computation and Cognition, Universidade Federal do ABC, Rua Santa Adelia, 166 - Santo Andre, 09210-170, Brazil; 3- Chemistry Institute, University of Sao Paulo, Av. Lineu Prestes, 748 - Sao Paulo, 05508-900; 4- Institute of Mathematics and Statistics, University of Sao Paulo, Rua do Matao, 1010 - Cidade Universitaria, 05508-090, Sao Paulo, Brazil

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:2005
PUBLICATION TYPE: journal
PUBLICATION NAME: BMC Genomics
ARTICLE TITLE: Comparison of gene expression profiles produced by CAGE, illumina microarray and Real Time RT-PCR
SUBMIT DATE: 2009-01-07
ACCEPT DATE:
PUBLICATION DATE:
TITLE: Comparison of gnee expression profiles produced by CAGE, illumina microarray and Real Time RT-PCR. (paper)
STATUS: Submitted
AUTHOR NAME: Andre Fujita1, Masao Nagasaki1, Seiya Imoto1, Ayumu Saito1, Emi Ikeda1, Teppei Shimamura1, Rui Yamaguchi1, Harukazu Suzuki2, Yoshihide Hayashizaki2, Satoru Miyano1
AUTHOR AFFILIATION: 1- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan; 2-Genome LSA Technology Development Unit, Omics ScienceCenter, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:2006
PUBLICATION TYPE: journal
PUBLICATION NAME: Bioinformatics
ARTICLE TITLE: Identification and quantification of Granger causality between sets of genes
SUBMIT DATE: 2009-03-16
ACCEPT DATE:
PUBLICATION DATE:
TITLE: Identification and quantification of Granger causality between sets of genes (paper)
STATUS: Submitted
AUTHOR NAME: Andre Fujita1, Joao Ricardo Sato2, Luciana Rodrigues Gomes3, Mari Cleide Sogayar3, Satoru Miyano1
AUTHOR AFFILIATION: 1- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan; 2-Center of Mathematics, Computation and Cognition, Universidade Federal do ABC, Rua Santa Adelia, 166 - Santo Andre, 09210-170, Brazil; 3- Chemistry Institute, University of Sao Paulo, Av. Lineu Prestes, 748 - Sao Paulo, 05508-900

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:2010
PUBLICATION TYPE: journal
PUBLICATION NAME: BMC Systems Biology, 2009
ARTICLE TITLE: Recursive regularization for inferring gene networks from time-course gene expression profiles
SUBMIT DATE: 2008-12-08
ACCEPT DATE:
PUBLICATION DATE: 2009-04-01
TITLE: Recursive regularization for inferring gene networks from time-course gene expression profiles
STATUS: Accepted
AUTHOR NAME: Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Andre Fujita, Masao Nagasaki, Satoru Miyano
AUTHOR AFFILIATION: Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan;

------------------------------ PUBLICATION ------------------------------
PUBLICATION ID:2011
PUBLICATION TYPE: journal
PUBLICATION NAME: BMC Systems Biology, 1:39, 2007
ARTICLE TITLE: Modeling gene expression regulatory networks with the sparse vector autoregressive model
SUBMIT DATE: 2007-08-30
ACCEPT DATE:
PUBLICATION DATE:
TITLE: Modeling gene expression regulatory networks with the sparse vector autoregressive model
STATUS: Published
AUTHOR NAME: Andre Fujita1, Joao Ricardo Sato2, Humberto Miguel Garay-Malpartida3, Rui Yamaguchi1, Mari Cleide Sogayar3, Carloes Eduardo Ferreira4, Satoru Miyano1
AUTHOR AFFILIATION: 1- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan; 2-Center of Mathematics, Computation and Cognition, Universidade Federal do ABC, Rua Santa Adelia, 166 - Santo Andre, 09210-170, Brazil; 3- Chemistry Institute, University of Sao Paulo, Av. Lineu Prestes, 748 - Sao Paulo, 05508-900; 4- Institute of Mathematics and Statistics, University of Sao Paulo, Rua do Matao, 1010 - Cidade Universitaria, 05508-090, Sao Paulo, Brazil

その他
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