Technology for analyzing biological functions from phenome

• Project/Area Number: 17017007
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The University of Tokyo
• Principal Investigator: MORISHITA Shinichi The University of Tokyo, 大学院・新領域創成科学研究科, 教授 (90292854)
• Co-Investigator(Kenkyū-buntansha): 瀬々 潤 東京大学, 大学院・情報理工学系研究科, 科学技術振興特任教員 (40361539)
• Project Period (FY): 2005 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥94,800,000 (Direct Cost: ¥94,800,000); Fiscal Year 2009: ¥19,200,000 (Direct Cost: ¥19,200,000); Fiscal Year 2008: ¥19,100,000 (Direct Cost: ¥19,100,000); Fiscal Year 2007: ¥18,900,000 (Direct Cost: ¥18,900,000); Fiscal Year 2006: ¥18,600,000 (Direct Cost: ¥18,600,000); Fiscal Year 2005: ¥19,000,000 (Direct Cost: ¥19,000,000)
• Keywords: ゲノム / バイオインフォマティクス / 表現型解析 / 画像処理 / 変異体 / 表現型 / バイオインフォマテイクス

Research Abstract

The goal of this research is understanding functions of DNA. Towards this end, we developed software for processing fruitfly mutant wing photographs to accelerate functional analysis of genes involved in cell growth. We also approached the problem using next-generation sequencers to reveal that the chromatin structure of DNA affects evolution considerably, which is the first study to uncover the property.

Research Products

• [Journal Article] Robust and Accurate Recognition of Veins in Fruit Fly Wings (2009)
  • Author(s): Hatsuda H, Muramatsu K, Aigaki T, Morishita S.
  • Journal Title: IEEE 6th International Symposium on Image and Signal Processing and Analysis Pages: 146-151
• [Journal Article] UTGB Toolkit for Personalized Genome Browsers (2009)
  • Author(s): Saito TL, Yoshimura J, Sasaki S, Ahsan B, Sasaki A, Kuroshu R, Morishita S.
  • Journal Title: Bioinformatics 25(15) Pages: 1856-1861
• [Journal Article] Efficient frequency-based de novo short read clustering for error trimming in next-generation sequencing (2009)
  • Author(s): Qu W, Hashimoto S, Morishita S.
  • Journal Title: Genome Research 19(7) Pages: 1309-1315
• [Journal Article] Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites (2009)
  • Author(s): Sasaki S, Mello C, Shimada A, Nakatani Y, Hashimoto S, Ogawa M, Matsushima K, Gu S G, Kasahara M, Ahsan B, Sasaki A, Saito T, Suzuki Y, Sugano S, Kohara Y, Takeda H, Fire A, Morishita S.
  • Journal Title: Science 323(5912) Pages: 401-404
• [Journal Article] MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database (2009)
  • Author(s): Ahsan B, Saito T, Hashimoto S, Muramatsu K, Tsuda M, Sasaki A, Matsushima K, Aigaki T, Morishita S.
  • Journal Title: Nucleic Acids Research Vol.37
• [Journal Article] High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer (2009)
  • Author(s): Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee C C, Nutter R C, Morishita S, Matsushima K.
  • Journal Title: PLoS One 4(1)
• [Journal Article] Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites (2009)
  • Author(s): Sasaki, et.al.
  • Journal Title: Science 323(5912) Pages: 401-404
  • Peer Reviewed
• [Journal Article] MachiBase : a Drosophila melanogaster 5'-end mRNA transcription database (2009)
  • Author(s): Ahsan, et.al.
  • Journal Title: Nucleic Acids Research 37 Pages: 49-53
  • Peer Reviewed
• [Journal Article] 5'-end transcriptome using a next generation DNA sequencer (2009)
  • Author(s): Hashimoto, et.al.
  • Journal Title: PLoS One 4(1) Pages: 4108-4108
  • Peer Reviewed
• [Journal Article] The genome of a lepidopteran model insect, the silkworm Bombyx mori. (2008)
  • Author(s): The International Silkworm Genome Consortium (Morishita S is one of the corresponding authors)
  • Journal Title: Insect Biochemistry and Molecular Biology 38(12) Pages: 1036-1045
• [Journal Article] Variant between CPT1B and CHKB associated with susceptibility to narcolepsy (2008)
  • Author(s): Miyagawa T, Kawashima M, Nishida N, Ohashi J, Kimura R, Fujimoto A, Shimada M, Morishita S, Shigeta T, Lin L, Hong SC, Faraco J, Shin YK, Jeong JH, Okazaki Y, Tsuji S, Honda M, Honda Y, Mignot E, Tokunaga K.
  • Journal Title: Nature Genetics 40(11) Pages: 1324-8
• [Journal Article] UTGB/medaka: genomic resource database for medaka biology (2008)
  • Author(s): Ahsan B, (36 authors), Morishita S.
  • Journal Title: Nucleic Acids Research 36
• [Journal Article] The genome of a lepidopteran model insect, the silkworm Bombyx mori (2008)
  • Author(s): The International Silkworm Genome Consortium
  • Journal Title: I Insect Biochemistry and Molecular Biology 38(12) Pages: 1046-1045
  • Peer Reviewed
• [Journal Article] UTGB/medaka: genomic resource database for medaka biolgoy (2008)
  • Author(s): Ahsan, et. al.
  • Journal Title: Nucleic Acids Research 36 Pages: 747-52
  • Peer Reviewed
• [Journal Article] Reconstruction of the Vertebrate Ancestral Genome Reveals Dynamic Genome Reorganization in Early Vertebrates (2007)
  • Author(s): Nakatani Y, Takeda H, Kohara Y, Morishita S.
  • Journal Title: Genome Research 17(9) Pages: 1254-1265
• [Journal Article] The medaka draft genome and insights into vertebrate genome evolution (2007)
  • Author(s): Kasahara M, (34 authors), Takeda H*, Morishita S*, Kohara Y*.
  • Journal Title: Nature 447 Pages: 714-719
• [Journal Article] The medaka draft genome and insights into vertebrate genome evolution (2007)
  • Author(s): Kasahara, et. al.
  • Journal Title: Nature 477 Pages: 714-719
  • Peer Reviewed
• [Journal Article] Reconstruction of the Vertebrate Ancestral Genome Reveals Dynamic Genome Reorganization in Early Vertebrates (2007)
  • Author(s): Nakatani, et. al.
  • Journal Title: Genome Research 17(9) Pages: 1254-1265
  • Peer Reviewed
• [Journal Article] A large-scale full-length cDNA analysis to explore the budding yeast transcriptome (2006)
  • Author(s): Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, Ito T.
  • Journal Title: Proc Natl Acad Sci U S A. 103(47) Pages: 17846-51
• [Journal Article] PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome (2006)
  • Author(s): T. Yamada, H. Souma, S. Morishita.
  • Journal Title: Nucleic Acids Research 34
• [Journal Article] Amoeba Join : Overcoming Structural Fluctuations of XML Data. (2006)
  • Author(s): Taro L.Saito, Shinichi Morishita
  • Journal Title: Ninth International Workshop on the Web and Databases (WebDB 2006). (online) Pages: 6-6
• [Journal Article] PrimerStation : a highly specific multiplex genomic PCR primer design server for the human genome. (2006)
  • Author(s): Tomoyuki Yamada, Haruhiko Souma, Shinichi Morishita
  • Journal Title: Nucl. Acids Res. 34
• [Journal Article] A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. (2006)
  • Author(s): Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, Ito T
  • Journal Title: Proc Natl Acad Sci U S A. 103(47) Pages: 17846-17851
• [Journal Article] High- dimensional and large-scale phenotyping of yeast mutants (2005)
  • Author(s): Ohya Y, (24 authors), Morishita S.
  • Journal Title: Proc Natl Acad Sci U S A. 102(52) Pages: 19015-20
• [Journal Article] Data Mining Tools for the Saccharomyces cerevisiae Morphological Database (2005)
  • Author(s): Saito TL, Sese J, Nakatani Y, Sano F, Yukawa M, Ohya Y, Morishita S.
  • Journal Title: Nucleic Acids Research 33
  • NAID: 120006811259
• [Journal Article] 5'SAGE: 5'-end Serial Analysis of Gene Expression database (2005)
  • Author(s): Kasai Y, Hashimoto S, Yamada T, Sese J, Sugano S, Matsushima K, Morishita S.
  • Journal Title: Nucleic Acids Research Database Issue 33
• [Journal Article] Accelerated off-target search algorithm for siRNA. (2005)
  • Author(s): Yamada T, Morishita S.
  • Journal Title: Bioinformatics 21(8) Pages: 1316-1324
• [Journal Article] dsCheck: highly sensitive off-target search software for dsRNA-mediated RNA interference (2005)
  • Author(s): Naito Y, Yamada T, Matsumiya T, Ui-Tei K, Saigo K, Morishita S.
  • Journal Title: Nucleic Acids Research 33
• [Journal Article] dsCheck : highly sensitive off-target search software for dsRNA-mediated RNA interference. (2005)
  • Author(s): Yuki Naito, Tomoyuki Yamada, Takahiro Matsumiya, Kumiko Ui-Tei, Kaoru Saigo, Shinichi Morishita
  • Journal Title: Nucleic Acids Research (Web Server Issue)
• [Journal Article] Accelerated off-target search algorithm for siRNA (2005)
  • Author(s): Tomoyuki Yamada, Shinichi Morishita
  • Journal Title: Bioinformatics 21(8) Pages: 1316-1324
• [Journal Article] 5'SAGE : 5' -end Serial Analysis of Gene Expression database. (2005)
  • Author(s): Yasuhiko Kasai, Shin-ichi Hashimoto, Tomoyuki Yamada, Jun Sese, Sumio Sugano, Kouji Matsushima, Shinichi Morishita
  • Journal Title: Nucl.Acids Res 33
• [Journal Article] Data Mining Tools for the Saccharomyces cerevisiae Morphological Database (2005)
  • Author(s): Taro L.Saito (*), Jun Sese(*), Yoichiro Nakatani, Fumi Sano, Masashi Yukawa, Yoshikazu Ohya, Shinichi Morishita
  • Journal Title: Nucleic Acids Research 33
  • NAID: 120006811259
• [Presentation] Chromatin- associated periodicity in genetic variation downstream of transcriptional start sites (2009)
  • Author(s): Shinichi Morishita
  • Organizer: The 8th International Workshop on Advanced Genomics
  • Place of Presentation: 東京
• [Book] 生命研究への応用と開発が進むバイオデータベースとソフトウェア最前線 (2008)
  • Author(s): 森下真一, 阿久津達也編
  • Total Pages: 226
  • Publisher: 実験医学
• [Book] Large-scale genome sequence processing. (2006)
  • Author(s): M. Kasahara, S. Morishita.
  • Total Pages: 248
  • Publisher: Imperial College Press
• [Book] Large-scale genome sequence processing. (2006)
  • Author(s): Kasahara, M., Morishita, S.
  • Total Pages: 248
  • Publisher: Imperial College Press
• [Remarks] UT Genome Browser (Yeast)出芽酵母ゲノムにおける転写開始点を完全長cDNAにより再アノテーションしたデータベースを公開。11, 575個の転写開始点が3, 638個の遺伝子と対応付けられており、出芽酵母においても複数の転写開始点が存在することが示されている
  • URL: http://yeast.utgenome.org/
• [Remarks] UT Genome Browser (Medaka)メダカゲノムブラウザー
  • URL: http://medaka.utgenome.org/
• [Remarks] SCMD (Saccharomyces Cerevisiae Morphological Database)出芽酵母の遺伝子破壊株(EUROSCARF)の顕微鏡画像をイメージ処理し、形態に関する様々な定量的パラメータを抽出。2001年末よりデータ収集を開始し、2004年8月に約5000個の非必須遺伝子破壊株、約180万細胞の形態パラメータの計測を完了
  • URL: http://yeast.gi.k.u-tokyo.ac.jp/
• [Remarks] siDirect (ヒト、マウス、ラット、ドッグ等のsiRNA配列設計サーバー)
  • URL: http://design.rnai.jp/
• [Remarks] PrimerStationマルチプレックスゲノミックpcrプライマ設計サイト。SNPタイピング, 絶対定量プライマ設計、オリゴプローブアレー設計等に利用可能
  • URL: http://ps.cb.k.u-tokyo.ac.jp/
• [Remarks] 5'SAGE (ヒト5SAGEタグブラウザー)5'-end SAGE tagがヒトゲノム上でどの位置に出現し、出現回数が何回あり、周辺にどのような遺伝子がエンコードされているかを、わかりやすく表示するweb server
  • URL: http://5sage.gi.k.u-tokyo.ac.jp/
• [Remarks] MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. ショウジョウバエの7つの組織(胚、幼虫、老/若x雄/雌, S2)から収集した各々3-400万個の転写開始点タグ情報の公開データベース
  • URL: http://machibase.gi.k.u-tokyo.ac.jp/
• [Remarks] DeNovoShortReadClustering FreClu 5'SAGEおよびmiRNA等の同じローカスから由来する短いタグ配列の誤りを訂正するためのソフトウエア。次世代シーケンサーが出力する数億個のタグ配列を高速に処理できるような線形時間アルゴリズムである
  • URL: http://mlab.cb.k.u-tokyo.ac.jp/~quwei/
• [Remarks] UTGB toolkit for personalized genome browsers. 各研究室レベルで容易にゲノム解析ができるように、Personalized Genome Browserを構築するツールキットを研究開発し、無料で公開した。実際数分でゲノムブラウザーを立ち上げ、データをsecureな環境で分析することも、一般に公開することも可能である
  • URL: http://utgenome.org/
• [Remarks] dsCheck線虫、ショウジョウバエ等のモデル生物においてRNA干渉を行う配列を設計するwebサイト。cross reactionを防止できるように配慮してある
  • URL: http://dscheck.rnai.jp/
• [Remarks] MuSICA2全長cDNA配列を求めるために、複数のcDNAクローンを短く断片化して、次世代シーケンサーで解読し、参照ゲノムへとアラインメントし、情報を補ってcDNA配列を解読するソフト
  • URL: http://musica.gi.k.u-tokyo.ac.jp/
• [Remarks] メダカゲノムブラウザー
  • URL: http://medaka.utgenome.org/
• [Remarks] 出芽酵母ゲノムブラウザー
  • URL: http://yeast.utgenome.org/
• [Remarks] siRNA設計
  • URL: http://design.rnai.jp/
• [Remarks] 出芽酵母表現型解析
  • URL: http://scmdgi.k.u-tokyo.ac.jp/
• [Remarks] Multiplex Gepomic PCR design
  • URL: http://ps.cb.k.urtokyo.ac.jp/
• [Remarks] ショウジョウバエゲノムブラウザー
  • URL: http://machibase.gi.k.u-tokyo.ac.jp/
• [Remarks] 1.メダカゲノムブラウザー
  • URL: http://medaka.utgenome.org/
• [Remarks] 2.出芽酵母ゲノムブラウザー
  • URL: http://yeast.utgenome.org/
• [Remarks] 3.siRNA設計
  • URL: http://design.rnai.jp/
• [Remarks] 4.出芽酵母表現型解析
  • URL: http://scmd.gi.k.u-tokyo.ac.jp/
• [Remarks] 5.Multiplex Genomic PCR design
  • URL: http://ps.cb.k.u-tokyo.ac.jp/