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Development of guidelines for transcriptome data analysis with long-reads

Research Project

Project/Area Number 15K06919
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field System genome science
Research InstitutionThe University of Tokyo

Principal Investigator

Kadota Koji  東京大学, 大学院農学生命科学研究科(農学部), 准教授 (60392221)

Research Collaborator Terada Tomoko  
Project Period (FY) 2015-10-21 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2017: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2016: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2015: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
KeywordsRNA-seq / 発現変動解析 / バイオインフォマティクス / R / トランスクリプトーム / クラスタリング / 発現変動
Outline of Final Research Achievements

In the life sciences field, researchers have investigated nucleotide sequences and expression levels of transcripts (called transcriptome) working in a sample that constitutes an organism. They include the measurement of expression similarities between samples and the identification of genes differentially expressed between conditions of interest. In this research, we proposed to use Silhouette scores to objectively estimate the degree of separation between groups of interest. We confirmed that silhouettes is useful for exploring data with predefined group labels. It would help provide both an objective evaluation of the sample clustering results and insights into the differential expression results with regard to the compared groups.

Academic Significance and Societal Importance of the Research Achievements

サンプル間の全体的な類似傾向を眺めるクラスタリングは、トランスクリプトームデータ解析において、必ずといっていいほどよく行われる作業である。しかしながら、得られる結果を都合よく主観的に評価することもできるため、任意のグルーピングにおける全体的な類似度を客観的に評価する必要性やその枠組みの提供は重要である。本研究で提案したシルエットスコアは、クラスタリング結果だけでなく、発現変動解析結果の解釈にも援用できるものであり意義深いものと考える。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (14 results)

All 2019 2018 2016 2015 Other

All Journal Article (5 results) (of which Peer Reviewed: 3 results,  Open Access: 5 results,  Acknowledgement Compliant: 3 results) Presentation (5 results) (of which Invited: 2 results) Remarks (4 results)

  • [Journal Article] TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data2019

    • Author(s)
      Su Wei、Sun Jianqiang、Shimizu Kentaro、Kadota Koji
    • Journal Title

      BMC Research Notes

      Volume: 12 Issue: 1 Pages: 133-133

    • DOI

      10.1186/s13104-019-4179-2

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Silhouette scores for arbitrary defined groups in gene expression data and insights into differential expression results.2018

    • Author(s)
      Zhao S, Sun J, Shimizu K, Kadota K
    • Journal Title

      Biol Proced Online

      Volume: 20 Issue: 1 Pages: 5-5

    • DOI

      10.1186/s12575-018-0067-8

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 次世代シーケンサーデータの解析手法:第7回ロングリードアセンブリ2016

    • Author(s)
      谷澤靖洋, 神沼英里, 中村保一, 遠野雅徳, 大崎研, 清水謙多郎, 門田幸二
    • Journal Title

      日本乳酸菌学会誌

      Volume: 27 Pages: 101-110

    • NAID

      130005773878

    • Related Report
      2016 Research-status Report
    • Open Access / Acknowledgement Compliant
  • [Journal Article] 次世代シーケンサーデータの解析手法:第8回アセンブリ後の解析2016

    • Author(s)
      谷澤靖洋, 神沼英里, 中村保一, 遠野雅徳, 寺田朋子, 清水謙多郎, 門田幸二
    • Journal Title

      日本乳酸菌学会誌

      Volume: 27 Pages: 187-195

    • NAID

      130006243121

    • Related Report
      2016 Research-status Report
    • Open Access / Acknowledgement Compliant
  • [Journal Article] Evaluation of methods for differential expression analysis on multi-group RNA-seq count data.2015

    • Author(s)
      Tang M, Sun J, Shimizu K, Kadota K
    • Journal Title

      BMC Bioinformatics

      Volume: 16 Issue: 1 Pages: 361-361

    • DOI

      10.1186/s12859-015-0794-7

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Rで塩基配列解析:ゲノム解析からトランスクリプトーム解析まで2016

    • Author(s)
      門田幸二
    • Organizer
      HPCI講習会・バイオインフォマティクス実習コース
    • Place of Presentation
      産総研・臨海副都心センター(東京)
    • Year and Date
      2016-03-03
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] NGS解析(中~上級)クラウド環境との連携、ロングリードデータの解析2016

    • Author(s)
      門田幸二
    • Organizer
      平成28年度NGSハンズオン講習会
    • Place of Presentation
      東京大学(東京都 文京区)
    • Related Report
      2016 Research-status Report
  • [Presentation] Benchmarking methods for simulation and analysis of RNA sequencing data.2015

    • Author(s)
      湯敏, 孫建強, 清水謙多郎, 門田幸二
    • Organizer
      生命医薬情報学連合大会2015年大会
    • Place of Presentation
      京都大学(京都)
    • Year and Date
      2015-10-29
    • Related Report
      2015 Research-status Report
  • [Presentation] DEGES-based method for estimating the gene dispersions of RNA-seq count data without replicate.2015

    • Author(s)
      孫建強, 湯敏, 清水謙多郎, 門田幸二
    • Organizer
      生命医薬情報学連合大会2015年大会
    • Place of Presentation
      京都大学(京都)
    • Year and Date
      2015-10-29
    • Related Report
      2015 Research-status Report
  • [Presentation] ビッグデータ解析の一例としてのトランスクリプトーム解析とその周辺2015

    • Author(s)
      門田幸二
    • Organizer
      日本臨床麻酔学会・第35回大会
    • Place of Presentation
      パシフィコ横浜(神奈川)
    • Year and Date
      2015-10-21
    • Related Report
      2015 Research-status Report
    • Invited
  • [Remarks]

    • URL

      http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html

    • Related Report
      2018 Annual Research Report
  • [Remarks]

    • URL

      https://github.com/swsoyee/TCC-GUI

    • Related Report
      2018 Annual Research Report
  • [Remarks] (Rで)塩基配列解析

    • URL

      http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html

    • Related Report
      2017 Research-status Report 2016 Research-status Report
  • [Remarks] (Rで)塩基配列解析

    • URL

      http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html

    • Related Report
      2015 Research-status Report

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Published: 2015-10-21   Modified: 2020-03-30  

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