Probabilistic Models of the Marginal Distribution of Gene Expression

• Project/Area Number: 19310128
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: 基礎ゲノム科学
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: HORTON Paul National Institute of Advanced Industrial Science and Technology, 生命情報工学研究センター, 研究チーム長 (00371071)
• Co-Investigator(Kenkyū-buntansha): HORIMOTO Katsuhisa 独立行政法人産業技術総合研究所, 生命情報工学研究センター, 研究チーム長 (40238803) ; ABURATANI Sachiyo 独立行政法人産業技術総合研究所, 生命情報工学研究センター, 研究員 (10361627)
• Project Period (FY): 2007 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥19,370,000 (Direct Cost: ¥14,900,000、Indirect Cost: ¥4,470,000); Fiscal Year 2009: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000); Fiscal Year 2008: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000); Fiscal Year 2007: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
• Keywords: 遺伝子発現 / 次世代シーケンサー / TSS-Seq法 / 転写頻度 / Quality Scores / 配列度数修正 / プロモータ解析 / 組織特異性 / 遺伝子分類 / 転写制御 / 発生の制御 / 細胞学 / 確率モデル / 確立モデル

Research Abstract

1) Established a method for automatically constructing probabilistic mixture models of gene expression from microarray data. 2) Performed analysis on the marginal distribution of genes and hypothesized that the noise in microarray experiments hinders proper analysis. 3) Established a method for correcting the influence of misreads to allow next-generation sequencer mRNA sequence data to be used for precise analysis of gene expression.

Research Products

• [Journal Article] RECOUNT, Next“Generation Sequencing Error Correction Tool (2009)
  • Author(s): Edward Wijaya, Martin Frith, Yutaka Suzuki, Paul Horton
  • Journal Title: Genome Informatics 23(1) Pages: 189-201
  • Peer Reviewed
• [Journal Article] Characterizing Genes by Marginal Expression Distribution (2009)
  • Author(s): Edward Wijaya, Paul Horton
  • Journal Title: Communications in Computer and Information Science 28 Pages: 164-175
  • Peer Reviewed
• [Journal Article] RECOUNT : Next Generation Sequencing Error Correction Tool (2009)
  • Author(s): Edward Wijaya, Martin Frith, Yutaka Suzuki, Paul Horton
  • Journal Title: Genome Informatics 1 Pages: 187-201
  • Peer Reviewed
• [Journal Article] ヌクレオソーム位置とその配列解析 (2008)
  • Author(s): Paul Horton
  • Journal Title: ファルマシア 44巻4号 Pages: 352-353
• [Journal Article] CellMontage:Similar EXPression Profile Search Server (2007)
  • Author(s): Wataru Fujibuchi
  • Journal Title: Bioi lformatics 23(no 22) Pages: 3103-3104
  • Peer Reviewed
• [Journal Article] WoLF PSORT:Protein Localization Pnedictor (2007)
  • Author(s): Paul Horton
  • Journal Title: Nucleic Acids Research Doi:10.1093
  • Peer Reviewed
• [Presentation] RECOUNT, Next Generation Sequencing Error Correction Tool (2009)
  • Author(s): Edward Wijaya, Martin C. Frith, Paul Horton
  • Organizer: 20th international Conference on Genome Informatics (GIW09)
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-15
• [Presentation] RECOUNT : Next Generation Sequencing Error Correction Tool (2009)
  • Author(s): Edward Wijaya
  • Organizer: Genome Informatics Workshop
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-15
• [Presentation] Characterizing Genes by Marginal Expression Distribution (2008)
  • Author(s): Edward Wijaya
  • Organizer: Proceedings of Bioscience and BioTechnology, BSBT2008 (査読有り国際学会)
  • Place of Presentation: 中国海南島三亜
  • Year and Date: 2008-12-14
• [Presentation] Characterizing Genes by Marginal Expression Distribution (2008)
  • Author(s): Edward Wijaya, Paul Horton
  • Organizer: Bioscience and Biotechnology (BSBT2008)
  • Place of Presentation: 海南、中国
  • Year and Date: 2008-12-13
• [Presentation] SHOE:Promoter Analysis Tool (2007)
  • Author(s): Natalia Poluliakh
  • Organizer: 21st International Mammalian Genome Conference
  • Place of Presentation: 京都
  • Year and Date: 2007-10-30
• [Book] "Computational Prediction of Subcellular Localization"in Methods Mol.Biol. (2007)
  • Author(s): Kenta Nakai
  • Total Pages: 37
  • Publisher: Humana Press,USA
• [Remarks]
  • URL: http://seq.cbrc.jp/recount/
• [Remarks]
  • URL: http://seq.cbrc.jp/recount/
• [Remarks]
  • URL: http://seq.cbrc.jp
• [Remarks]
  • URL: http://seq.cbrc.jp