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Network Analysis from microarray data

Research Project

Project/Area Number 12206008
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKyushu University

Principal Investigator

KUHARA Satoru  Kyushu University, Faculty of Agriculture, Professor, 大学院農学研究院, 教授 (00153320)

Co-Investigator(Kenkyū-buntansha) TASHTO Kousuke  Kyushu University, Faculty of Agriculture, Associate Professor, 大学院農学研究院, 助教授 (00192170)
ONISHI Sadanori  Kyushu University, Faculty of Agriculture, Professor, 大学院数理学府, 教授 (40090550)
MARUYAMA Osamu  Kyushu University, Faculty of Agriculture, Associate Professor, 大学院数理学府, 助教授 (20282519)
篠原 歩  九州大学, 大学院・システム情報科学研究院, 助教授 (00226151)
中野 幸二  九州大学, 大学院・工学研究院, 助教授 (10180324)
Project Period (FY) 2005
Project Status Completed (Fiscal Year 2005)
Budget Amount *help
¥53,800,000 (Direct Cost: ¥53,800,000)
Fiscal Year 2004: ¥12,800,000 (Direct Cost: ¥12,800,000)
Fiscal Year 2003: ¥12,000,000 (Direct Cost: ¥12,000,000)
Fiscal Year 2002: ¥13,500,000 (Direct Cost: ¥13,500,000)
Fiscal Year 2001: ¥15,500,000 (Direct Cost: ¥15,500,000)
KeywordsBioinformatics / Genome / Informatics / Expression control / Microarray / DNAマイクロアレイ / 遺伝子発現制御 / 発現制御ネットワーク / 出芽酵母 / モデリング / DNA-蛋白質相互作用 / プロモーターチップ / 微小電極 / バイオインフォマティクス / 電気化学検出 / 転写因子
Research Abstract

Microarray techniques provide new insights into molecular classification of cancer types, which is critical for cancer treatments and diagnosis. Recently, an increasing number of supervised machine learning methods have been applied to cancer classification problems using gene expression data. Support vector machines (SVMs), in particular, have become one of the most effective and leading methods. However, there exist few studies on the application of other kernel methods in the literature. We apply a kernel subspace (KS) method to multiclass cancer classification problems, and assess its validity by comparing it with multiclass SVMs. Our comparative study using seven multiclass cancer datasets demonstrates that the KS method has high performance that is comparable to multiclass SVMs. Furthermore, we propose an effective criterion for kernel parameter selection, which is shown to be useful for the computation of the KS method.
Microarrays pose a great challenge on the data analysis, bec … More ause the number of genes often exceeds tens of thousands, whereas the number of samples available is at most a few hundred. In microarray data analysis, gene selection has been a central issue in recent years. Gene selection plays several important tasks. If it is possible to identify a small subset of biological relevant genes, it may provide insights into understanding the underlying mechanism of a certain biological phenomenon. In general, gene selection can be performed in different manners: the filter and wrapper approaches. We propose a new filter approach to gene subset selection for kernel-based methods. Our major goal is to enhance the performance of kernel-based classifiers without resorting to the wrapper approach. This can be realized by direct performing classification in the same feature space. It is different from the conventional filter approach combined with kernel-based classifier, where gene subset selection is performed in input space. We show that several well-known class separability criteria can be kernelized. Gene subset selection is performed based on the kernelized criteria. Our strategy is assessed by combining it with three kernel-based classifiers, from simple to advanced ones. We apply it to cancer classification problems on acute lymphoblastic leukemia and demonstrate validity of our proposed strategy by comparing it with several methods. Less

Report

(6 results)
  • 2005 Final Research Report Summary
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • 2002 Annual Research Report
  • 2001 Annual Research Report
  • 2000 Annual Research Report
  • Research Products

    (30 results)

All 2005 2004 Other

All Journal Article (9 results) Publications (21 results)

  • [Journal Article] MULTICLASS MOLECULAR CANCER CLASSIFICATION BY KERNEL SUBSPACE METHODS WITH EFFECTIVE KERNEL PARAMETER SELECTION2005

    • Author(s)
      S.Niijima
    • Journal Title

      Journal of Bioinformatics and Computational Biology 3

      Pages: 1071-1088

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] MULTICLASS MOLECULAR CANCER CLASSIFICATION BY KERNEL SUBSPACEMETHODS WITH EFFECTIVE KERNEL PARAMETER SELECTION.2005

    • Author(s)
      S.Niijima, S.Kuhara
    • Journal Title

      Journal of Bioinformatics and Computational Biology 3

      Pages: 1071-1088

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Detection and Normalization of Biases Present in Spotted cDNA Microarray Data : a composite method addressing dye, intensity-dependent, spatially-dependent, and print-order biases2005

    • Author(s)
      S.Uchida
    • Journal Title

      DNA Research 12(In press)

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Nucleotide substitutions in Staphylococcus aureus strains, Mu50,Mu3, and N315.2005

    • Author(s)
      T.Ohta
    • Journal Title

      DNA Research 11

      Pages: 51-56

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Reconstructing Phylogenetic Trees of Prokaryote Genomes by Randomly Sampling Oligopeptides2005

    • Author(s)
      O.Maruyama
    • Journal Title

      Proceedings of the 2005 International Workshop on Bioinformatics Research and Applications (In press)

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Functional Discriminant Analysis for Microarray Gene Expression Data Via Radial Basis Function Networks2004

    • Author(s)
      Y.Araki
    • Journal Title

      COMPSTAT 2004 Symposium

      Pages: 613-620

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Use of segment-based microarray in the analysis of global gene expression in response to various environmental stresses in the cyanobacterium Anabaena sp. FCC 71202004

    • Author(s)
      N.Sato, M.Ohmori, M.Ikeuchi
    • Journal Title

      J Gen Appl Microbiol. 50

      Pages: 1-8

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Gene subset selection in kernel-induced feature space

    • Author(s)
      S.Niijima
    • Journal Title

      Pattern Recognition letters (In press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Gene subset selection in kernel-induced feature space.

    • Author(s)
      S.Niijima, S.Kuhara
    • Journal Title

      Pattern Recognition letters (In press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Publications] D.Shinozaki, T.Akutsu, O.Maruyama: "Finding optimal degenerate patterns in DNA sequences"Bioinformatics. 19. ii206 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] S.Imoto, S.Kim, T.Goto, S.Aburatani, K.Tashiro, S.Kuhara, S.Miyano: "Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network"Journal of Bioinformatics and Computational Biology. 1. 231 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] S.Imoto, C.J.Savoie, S.Aburatani, S.Kim, K.Tashiro, S.Kuhara, S.Miyano: "Use of gene networks for identifying and validating drug targets"Journal of Bioinformatics and Computational Biology. 1. 459 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] S.Aburatani, K.Tashiro, C.J.Savoie, M.Nishizawa, K.hayashi, Y.Ito, S.Muta, K.Yamamoto, A.Enomoto, M.Masaki, S.Watanabe, Y.Maki, Y.takahashi, Y.Eguchi, Y.Sakaki, s.kuhara: "Discovery of Novel Transcription Control Relationships with Gene Regulatory Networks Generated from Multiple-disruption Full Genome Expression Libraries"DNA RESEARCH. 10(in press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] C.J.Savoie, S.Aburatani, S.Watanabe, Y.Eguchi, S.Muta, S.Imoto, S.Miyano, S.Kuhara, K.Tshiro: "Use of Gene Network from Full Genome Microarray Libraries to Identify Functionally Relevant Drug-affected Genes and Gene Regulation Cascades"DNA RESEARCH. 10(in press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] 伊藤隆司, 田代康介, 久原哲: "酵母ゲノムの体系的機能解析:発現制御ネットワーク、蛋白質間相互作用ネットワーク"蛋白質核酸酵素. 46. 2407-2413 (2001)

    • Related Report
      2002 Annual Research Report
  • [Publications] M.Maeda, T.Shibata, M.Nakayama, K.Nakano: "Gene Sensor Usng Functional Polymers"Technical Digest of the 18th Sensor Symposium 2001. 381-386 (2001)

    • Related Report
      2002 Annual Research Report
  • [Publications] M.Nakayama, T.Ihara, K.Nakano, M.Maeda: "DNA sensors using a ferrocene-oligonucleotide conjugate"Talanta. (in press). (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] O.Maruyama, T.Shoudai, E.Furuichi, S.Kuhara, S.Miyano: "Learning conformation rules"Discovery Science K.p.Jantke and A.Shinohara(eds.). 243-257 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 久原哲: "ゲノム解析を支える技術-DNAチップとその応用"電子情報通信学会. 84. 346-351 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 伊藤隆司, 田代康介, 久原哲: "酵母ゲノムの体系的機能解析:発現制御ネットワーク、蛋白質間相互作用ネットワーク"蛋白質核酸酵素. 46. 2407-2413 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] M.Maeda, T.Shibata, M.Nakayama, K.Nakano: "Gene Sensor Usng Functional Polymers"Technical Digest of the 18th Sensor Symposium 2001. 381-386 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] M.Nakayama, T.Ihara, K.Nakano, M.Maeda: "DNA sensors using a ferrocene-oligonucleotide conjugate"Talanta. (In press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Akutu,T., et. al.: "Algorithms for identifying Boolean networks andrelated bilogical networks based on matrix multiplication and function"Proc.of Fourth Annual Int.Conference on Comp.Molecular Biology. (in press). 8-14 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Nakano,K., et. al.: "DNA biosenser : Immunosensor Application for Anti-DNA Antiboy"American Chemical Society Symp.Series. (in press). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Ihara,T., et. al.: "Electrochmical Gene Sensor"American Chemical Society Symp.Series. (in press). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] 中野幸二: "DNAバイオセンサー"ぶんせき. 6. 125-133 (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Akutsu,T., et. al.: "Inferring qualitative relations in genetic networks and metabolic pathways"Bioinformatics. 168. 723-734 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Akutsu,T., et. al.: "Algorithms for identifying Boolean networks and related bilogical networks based on matrix multiplication and fingerprint function"J.Computational Biology. 7. 331-343 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] 久原哲: "ゲノム機能(松原,榊編集)発現プロファイルとトランスクリプトーム"中山書店. 25-39 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Nakano,K.: "Molecular recognition of DNA and Biosensor Applications, in A.G.Yolkov Ed, "Liquid Interfaces in Chemical, Biological and Pharmaceutical Applictions""Marceol Dekker. 515-532 (2001)

    • Related Report
      2000 Annual Research Report

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Published: 2001-04-01   Modified: 2018-03-28  

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