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Development of an integrated platform for analysis of epigenome and single-cell data

Planned Research

Project AreaIntegrated analysis and regulation of cellular diversity
Project/Area Number 17H06331
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionThe University of Tokyo

Principal Investigator

Nakato Ryuichiro  東京大学, 定量生命科学研究所, 講師 (60583044)

Project Period (FY) 2017-06-30 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥58,630,000 (Direct Cost: ¥45,100,000、Indirect Cost: ¥13,530,000)
Fiscal Year 2021: ¥10,660,000 (Direct Cost: ¥8,200,000、Indirect Cost: ¥2,460,000)
Fiscal Year 2020: ¥10,660,000 (Direct Cost: ¥8,200,000、Indirect Cost: ¥2,460,000)
Fiscal Year 2019: ¥10,660,000 (Direct Cost: ¥8,200,000、Indirect Cost: ¥2,460,000)
Fiscal Year 2018: ¥10,660,000 (Direct Cost: ¥8,200,000、Indirect Cost: ¥2,460,000)
Fiscal Year 2017: ¥15,990,000 (Direct Cost: ¥12,300,000、Indirect Cost: ¥3,690,000)
Keywordsシングルセル解析 / 立体構造解析 / 次世代シーケンサー / データ駆動型解析 / バイオインフォマティクス / 軌道解析 / 解析パイプライン / 1細胞解析 / 遺伝子ネットワーク / 疑似時系列解析 / 生命情報学 / エピゲノム / Data imputation / 情報基盤整備 / 大規模解析 / 数理モデリング
Outline of Final Research Achievements

This study aims to develop a robust system that enables the integrated analysis and visualization of large-scale data including single-cell and bulk assays and to contribute to identifying novel biological insights in the collaboration with other groups. We have developed 1) a robust method for detecting and comparing communities in gene co-expression networks constructed from single-cell transcriptome data, which could detect novel candidate marker genes of cancer stem cells, 2) a comprehensive and user-friendly platform for single-cell analysis and contribution to the biological analysis of other groups, and 3) a strategy and tools for large-scale bulk epigenome analysis and genome conformation analysis. The resources and developed tools have been published and publicly available.

Academic Significance and Societal Importance of the Research Achievements

シングルセル解析は世界中で用いられている重要な手法であるが、技術的な限界から得られるデータは精度が限られてしまう。本研究で開発した遺伝子ネットワーク推定手法はそのような疎なデータにも精度良く適用可能であり、シングルセル解析の有用性を更に高めるものである。また、本研究で構築した解析パイプラインにより、情報学が専門でない生命系研究者にとってのシングルセル解析のハードルを大きく低減し、領域内外の研究を推進することができた。共同研究で得たフィードバックをもとにパイプラインを更に改良し、世界的に競争が激しいシングルセル分野の最先端を反映した解析環境を提供している。

Report

(6 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (34 results)

All 2022 2021 2020 2019 2018 Other

All Journal Article (16 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 13 results,  Open Access: 15 results) Presentation (11 results) (of which Int'l Joint Research: 1 results,  Invited: 2 results) Book (3 results) Remarks (4 results)

  • [Journal Article] The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR‐Cas9 screen2022

    • Author(s)
      Cona Brandon、Hayashi Tomoatsu、Yamada Ai、Shimizu Naomi、Yokota Naoko、Nakato Ryuichiro、Shirahige Katsuhiko、Akiyama Tetsu
    • Journal Title

      FEBS Open Bio

      Volume: 12 Issue: 3 Pages: 582-593

    • DOI

      10.1002/2211-5463.13358

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data2021

    • Author(s)
      Nakajima N, Hayashi T, Fujiki K, Shirahige K, Akiyama T, Akutsu T, Nakato R.
    • Journal Title

      Nucleic Acids Res

      Volume: 49 Issue: 18 Pages: e104-e104

    • DOI

      10.1093/nar/gkab601

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Databases for Protein-Protein Interactions2021

    • Author(s)
      Nakajima Natsu、Akutsu Tatsuya、Nakato Ryuichiro
    • Journal Title

      Methods in Molecular Biology

      Volume: - Pages: 229-248

    • DOI

      10.1007/978-1-0716-1641-3_14

    • ISBN
      9781071616406, 9781071616413
    • Related Report
      2021 Annual Research Report
    • Open Access
  • [Journal Article] HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data2021

    • Author(s)
      Wang Jiankang、Nakato Ryuichiro
    • Journal Title

      Briefings in Bioinformatics

      Volume: 23 Issue: 1

    • DOI

      10.1093/bib/bbab509

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of human iPSC-derived quiescent hepatic stellate cell-like cells for drug discovery and in vitro disease modeling2021

    • Author(s)
      Koui Yuta、Himeno Misao、Mori Yusuke、Nakano Yasuhiro、Saijou Eiko、Tanimizu Naoki、Kamiya Yoshiko、Anzai Hiroko、Maeda Natsuki、Wang Luyao、Yamada Tadanori、Sakai Yasuyuki、Nakato Ryuichiro、Miyajima Atsushi、Kido Taketomo
    • Journal Title

      Stem Cell Reports

      Volume: 16 Issue: 12 Pages: 3050-3063

    • DOI

      10.1016/j.stemcr.2021.11.002

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data2021

    • Author(s)
      Nakajima N, Hayashi T, Fujiki K, Shirahige K, Akiyama T, Akutsu T, Nakato R.
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/2021.03.15.435370

    • Related Report
      2020 Annual Research Report
    • Open Access
  • [Journal Article] Transcription and replication organize cohesin-dependent chromosome loops2020

    • Author(s)
      Jeppsson K, Sakata T, Nakato R, Milanova S, Shirahige K, Bjoerkegren C.
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/2020.12.16.423068

    • Related Report
      2020 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Toward understanding the dynamic state of 3D genome2020

    • Author(s)
      Shinkai S, Onami S, Nakato R.
    • Journal Title

      Computational and Structural Biotechnology Journal

      Volume: 18 Pages: 2259-2269

    • DOI

      10.1016/j.csbj.2020.08.014

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity2020

    • Author(s)
      Tanaka, S. Ise, W. Inoue, T. Ito, A. Ono, C. Shima, Y. Sakakibara, S. Nakayama, M. Fujii, K. Miura, I. Sharif, J. Koseki, H. Koni, P. A. Raman, I. Li, Q. Z. Kubo, M. Fujiki, K. Nakato, R. Shirahige, K. Araki, H. Miura, F. Ito, T. Kawakami, E. Baba, Y. Kurosaki, T.
    • Journal Title

      Nature Immunology

      Volume: 21 Issue: 8 Pages: 950-961

    • DOI

      10.1038/s41590-020-0700-y

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Paternal restraint stress affects offspring metabolism via ATF-2 dependent mechanisms in Drosophila melanogaster germ cells2020

    • Author(s)
      Seong KH, Ly NH, Katou Y, Yokota N, Nakato R, Murakami S, Hirayama A, Fukuda S, Kang S, Soga T, Shirahige K, Ishii S.
    • Journal Title

      Communications Biology

      Volume: 3 Issue: 1

    • DOI

      10.1038/s42003-020-0992-3

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Methods for ChIP-seq analysis: A practical workflow and advanced applications2020

    • Author(s)
      Ryuichiro Nakato, Toyonori Sakata
    • Journal Title

      Methods

      Volume: Epub ahead of print Pages: 44-53

    • DOI

      10.1016/j.ymeth.2020.03.005

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] PHi-C: deciphering Hi-C data into polymer dynamics2020

    • Author(s)
      Shinkai Soya、Nakagawa Masaki、Sugawara Takeshi、Togashi Yuichi、Ochiai Hiroshi、Nakato Ryuichiro、Taniguchi Yuichi、Onami Shuichi
    • Journal Title

      NAR Genomics and Bioinformatics

      Volume: 2 Issue: 2

    • DOI

      10.1093/nargab/lqaa020

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells2019

    • Author(s)
      Nakato R, Wada Y, Nakaki R, Nagae G, Katou Y, Tsutsumi S, Nakajima N, Fukuhara H, Iguchi A, Kohro T, Kanki Y, Saito Y, Kobayashi M, Izumi-Taguchi A, Osato N, Tatsuno K, Kamio A, Hayashi-Takanaka Y, Wada H, Ohta S, Aikawa M, Nakajima H, Nakamura M, McGee RC, Heppner KW, Kawakatsu T, Genno M, Yanase H, Kume H, et al.
    • Journal Title

      Epigenetics & Chromatin

      Volume: 12 Issue: 1 Pages: 77-77

    • DOI

      10.1186/s13072-019-0319-0

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Missense Mutations in NKAP Cause a Disorder of Transcriptional Regulation Characterized by Marfanoid Habitus and Cognitive Impairment2019

    • Author(s)
      Fiordaliso Sarah K.、.....Shirahige Katsuhiko、Izumi Kosuke
    • Journal Title

      The American Journal of Human Genetics

      Volume: 105 Issue: 5 Pages: 987-995

    • DOI

      10.1016/j.ajhg.2019.09.009

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The novel lncRNA CALIC upregulates AXL to promote colon cancer metastasis2019

    • Author(s)
      Kawasaki Y、Miyamoto M、Oda T、Matsumura K、Negishi L、Nakato R、Suda S、Yokota N、Shirahige K、Akiyama T.
    • Journal Title

      EMBO reports

      Volume: 20 Issue: 8

    • DOI

      10.15252/embr.201847052

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile2018

    • Author(s)
      Ryuichiro Nakato, Katsuhiko Shirahige
    • Journal Title

      Bioinformatics

      Volume: 印刷中

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Presentation] Integrative study of hepatic fibrosis resolution mechanisms using single-cell RNA sequencing2021

    • Author(s)
      Eiko Saijou, Ryuichiro Nakato
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Single-cell RNA trajectory to infer dedifferentiation in Drosophila midgut2021

    • Author(s)
      Luis Augusto Eijy Nagai, Hiroki Nagai, Yuichiro Nakajima, Ryuichiro Nakato
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data2021

    • Author(s)
      Natsu Nakajima, Tomoatsu Hayashi, Katsunori Fujiki, Katsuhiko Shirahige, Tetsu Akiyama, Tatsuya Akutsu, Ryuichiro Nakato
    • Organizer
      第10回生命医薬情報学連合大会 (IIBMP2021)
    • Related Report
      2021 Annual Research Report
  • [Presentation] Identifying mutually exclusive gene sets from sparse scRNA-seq data2020

    • Author(s)
      Nakajima N., Hayashi T., Akiyama T., Akutsu T. and Nakato R.
    • Organizer
      第43回日本分子生物学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Large-scale analysis of multi-omics data toward the elucidation of epigenomic diversity2020

    • Author(s)
      中戸 隆一郎
    • Organizer
      第2回 ASHBi数理生物研究集会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 群雄割拠のシングルセル情報解析:現状把握とその先2020

    • Author(s)
      中戸 隆一郎
    • Organizer
      第9回生命医薬情報学連合大会 (IIBMP2020)
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] シングルセル解析のための情報解析技術の現状と展望2019

    • Author(s)
      中戸 隆一郎
    • Organizer
      第42回日本分子生物学会年会, ワークショップ「細胞社会ダイバーシティーの統合的解明と制御に挑む1細胞・1分子計測の数理科学」(兼オーガナイザー)
    • Related Report
      2019 Annual Research Report
  • [Presentation] Integrated analysis of gene expression and chromatin folding regulated by cohesin, cohesin loader and CTCF2019

    • Author(s)
      Ryuichiro Nakato
    • Organizer
      第13回国際ゲノム会議
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] シングルセルRNA-seqのためのデータ高感度化及び数理モデリング手法の開発2018

    • Author(s)
      中戸隆一郎
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] シングルセルデータから得られた遺伝子共発現ネットワークの比較解析2018

    • Author(s)
      仲嶋なつ, 林寛敦, 藤木克則, 秋山徹, 白髭克彦, 中戸隆一郎
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Comparative analysis of gene co-expression networks of Glioblastoma2018

    • Author(s)
      仲嶋なつ, 中戸隆一郎
    • Organizer
      日本バイオインフォマティクス学会年会
    • Related Report
      2018 Annual Research Report
  • [Book] Dockerプラットフォームを用いたシングルセル解析支援2021

    • Author(s)
      中戸 隆一郎
    • Total Pages
      7
    • Publisher
      羊土社
    • ISBN
      9784758103961
    • Related Report
      2021 Annual Research Report
  • [Book] 実験医学別冊 クロマチン解析実践プロトコール2020

    • Author(s)
      中戸 隆一郎
    • Total Pages
      6
    • Publisher
      羊土社
    • ISBN
      9784758122481
    • Related Report
      2020 Annual Research Report
  • [Book] シングルセルRNA-seq情報解析最前線2019

    • Author(s)
      中戸 隆一郎
    • Total Pages
      7
    • Publisher
      羊土社
    • ISBN
      9784758103831
    • Related Report
      2019 Annual Research Report
  • [Remarks] 1細胞解析技術講習会資料

    • URL

      https://singlecellanalysistutorial.readthedocs.io/en/latest/

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
  • [Remarks] singlecell_jupyter (DockerHub)

    • URL

      https://hub.docker.com/r/rnakato/singlecell_jupyter

    • Related Report
      2020 Annual Research Report
  • [Remarks] ヒト血管内皮エピゲノムデータベース

    • URL

      https://rnakato.github.io/HumanEndothelialEpigenome/

    • Related Report
      2019 Annual Research Report
  • [Remarks] 1細胞解析パイプラインDockerイメージ

    • URL

      https://hub.docker.com/r/rnakato/singlecell_jupyter

    • Related Report
      2019 Annual Research Report

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Published: 2017-07-04   Modified: 2023-01-30  

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