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Bioinformatics analysis of disease attractors and gene regulatory networks of Alzheimer's disease

Research Project

Project/Area Number 16K00385
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionTohoku University

Principal Investigator

Ogishima Soichi  東北大学, 東北メディカル・メガバンク機構, 教授 (40447496)

Project Period (FY) 2016-04-01 – 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 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywords生命情報 / 疾患アトラクター / アルツハイマー病 / 遺伝子調節ネットワーク / アルツハイマー
Outline of Final Research Achievements

We inferred attractors of disease state of Alzheimer’s disease (AD), conducted trajectory analysis of those attractors, and analyzed gene regulatory network forming those attractors. We then developed the algorithm to detect complex gene-environment (GxE) interactions causing AD. Using gene expression data of AD samples, we inferred probabilistic potentials of AD samples in the state space of AD gene expression data. We also inferred the corresponding gene regulatory network to AD attractors on probabilistic potentials.

Academic Significance and Societal Importance of the Research Achievements

本研究は遺伝要因、環境要因が複雑に相互作用して発症する多因子疾患の機序の解明に向けて、アルツハイマー病において遺伝要因、生活習慣や環境暴露等の環境要因の複雑な相互作用(G×E)の推定手法の開発を行い、遺伝子発現の状態空間における細胞集団の遺伝子発現ポテンシャルの推定、疾患アトラクターの推定、疾患アトラクターを形成する遺伝子調節ネットワークの解析を行った。遺伝要因、環境要因が複雑に相互作用して発症する多因子疾患の機序を解明することに寄与する、新たな情報学的な手法を開発した。

Report

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

    (46 results)

All 2019 2018 2017 2016

All Journal Article (17 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 17 results,  Open Access: 17 results,  Acknowledgement Compliant: 1 results) Presentation (26 results) (of which Int'l Joint Research: 5 results,  Invited: 13 results) Book (3 results)

  • [Journal Article] Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals2019

    • Author(s)
      Yamaguchi-Kabata, Y.,(途中略),Koshiba, S., (途中略), Tohoku Medical Megabank Project Study Group.(合計19名、本研究者は5番目)
    • Journal Title

      Hum. Genet.

      Volume: 印刷中 Issue: 4 Pages: 389-409

    • DOI

      10.1007/s00439-019-01998-7

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Novel Risk Loci Identified in a Genome-Wide Association Study of Urolithiasis in a Japanese Population2019

    • Author(s)
      Tanikawa Chizu、...、Ogishima Soichi、...、Matsuda Koichi
    • Journal Title

      Journal of the American Society of Nephrology

      Volume: 印刷中 Issue: 5 Pages: 855-864

    • DOI

      10.1681/asn.2018090942

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Serum magnesium and calcium levels in relation to ischemic stroke2019

    • Author(s)
      Larsson Susanna C.、Traylor Matthew、Burgess Stephen、Boncoraglio Giorgio B.、Jern Christina、Micha?lsson Karl、Markus Hugh S.、for the MEGASTROKE project of the International Stroke Genetics Consortium
    • Journal Title

      Neurology

      Volume: 92 Issue: 9

    • DOI

      10.1212/wnl.0000000000007001

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Maternity Log study: A longitudinal lifelog monitoring and multiomics analysis for the early prediction of complicated pregnancy2019

    • Author(s)
      Sugawara J, Ochi D, Yamashita R, Yamauchi T, Saigusa D, Wagata M, Obara T, Ishikuro M, Tsunemoto Y, 18名略, Hiyama S, Nagasaki M
    • Journal Title

      BMJ Open

      Volume: 9 Issue: 2 Pages: e025939-e025939

    • DOI

      10.1136/bmjopen-2018-025939

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Susceptibility Loci for Tanning Ability in the Japanese?Population Identified by a?Genome-Wide?Association Study from the Tohoku Medical Megabank Project Cohort Study2019

    • Author(s)
      Shido Kosuke、Kojima Kaname、Yamasaki Kenshi、Hozawa Atsushi、Tamiya Gen、Ogishima Soichi、Minegishi Naoko、Kawai Yosuke、Tanno Kozo、Suzuki Yoichi、Nagasaki Masao、Aiba Setsuya
    • Journal Title

      Journal of Investigative Dermatology

      Volume: epub Issue: 7 Pages: 1605-1608.e13

    • DOI

      10.1016/j.jid.2019.01.015

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare2018

    • Author(s)
      Yasuda Jun、Kinoshita Kengo、et al.,
    • Journal Title

      The Journal of Biochemistry

      Volume: 165 Issue: 2 Pages: 139

    • DOI

      10.1093/jb/mvy096

    • NAID

      40021809939

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Authentication of Patients and Participants in Health Information Exchange and Consent for Medical Research: A Key Step for Privacy Protection, Respect for Autonomy, and Trustworthiness2018

    • Author(s)
      Kogetsu Atsushi、Ogishima Soichi、Kato Kazuto
    • Journal Title

      Frontiers in Genetics

      Volume: 9 Pages: 167-167

    • DOI

      10.3389/fgene.2018.00167

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project2018

    • Author(s)
      Koshiba, S., (途中略), Yamamoto, M.(合計21名、本研究者は1番目)
    • Journal Title

      Genes Cells

      Volume: 23 Issue: 6 Pages: 406

    • DOI

      10.1111/gtc.12588

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes2018

    • Author(s)
      Malik R, Chauhan G, Traylor M, Minegishi N, AFGen Consortium,BioBank Japan Cooperative Hospital Group; MEGASTROKE Consortium
    • Journal Title

      Nat Genet

      Volume: 50 Issue: 4 Pages: 524-537

    • DOI

      10.1038/s41588-018-0058-3

    • Related Report
      2018 Annual Research Report 2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals article2018

    • Author(s)
      Y Yamaguchi-Kabata, J Yasuda, O Tanabe, Y Suzuki, H Kawame, N Fuse, M Nagasaki, Y Kawai, K Kojima, F Katsuoka, S Saito, I Danjoh, I Motoike, R Yamashita, S Koshiba, D Saigusa, G Tamiya, S Kure, N Yaegashi, Y Kawaguchi, F Nagami, S Kuriyama, J Sugawara, N Minegishi, A Hozawa, T Takai-Igarashi, K Kinoshita, M Yamamoto.
    • Journal Title

      Journal of Human Genetics.

      Volume: 63 Issue: 2 Pages: 213

    • DOI

      10.1038/s10038-017-0347-1

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Identification of six novel genetic loci associated with atrial fibrillation in Japanese population.2017

    • Author(s)
      Low SK, Takahashi A, Ebana Y, Ozaki K, Christophersen IE, Ellinor PT, AFGen Consortium, Ogishima S, Yamamoto M, Satoh M, Sasaki M, Yamaji T, Iwasaki M, Tsugane S, Tanaka K, Naito M, Wakai K, Tanaka H, Furukawa T, Kubo M, Ito K, Kamatani Y, Tanaka T.
    • Journal Title

      Nature Genetics

      Volume: - Issue: 6 Pages: 953-958

    • DOI

      10.1038/ng.3842

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design2017

    • Author(s)
      Takai-Igarashi T, Kinoshita K, Nagasaki M, Ogishima S, Nakamura N, Nagase S, Nagaie S, Saito T, Nagami F, Minegishi N, Suzuki Y, Suzuki K, Hashizume H, Kuriyama S, Hozawa A, Yaegashi N, Kure S, Tamiya G, Kawaguchi Y, Tanaka H, Yamamoto M
    • Journal Title

      BMC Med Inform Decis Mak

      Volume: 17 Issue: 1 Pages: 100-100

    • DOI

      10.1186/s12911-017-0494-5

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] FANTOM5 CAGE profiles of human and mouse samples2017

    • Author(s)
      Noguchi Shuhei、Arakawa Takahiro、Ogishima Soichi、ほか
    • Journal Title

      Sci Data

      Volume: 4 Issue: 1 Pages: 170112-170112

    • DOI

      10.1038/sdata.2017.112

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The Human Phenotype Ontology in 2017.2017

    • Author(s)
      Kohler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Ayme S, Baynam G, Bello SM, ... Ogishima S, ...Haendel M.
    • Journal Title

      Nucleic Acids Res

      Volume: 45(D1) Issue: D1 Pages: D865-D876

    • DOI

      10.1093/nar/gkw1039

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The Tohoku Medical Megabank Project: Design and Mission2016

    • Author(s)
      Kuriyama S, Yaegashi N, et al. (Tamiya G; 11th in 58 authors)
    • Journal Title

      Journal of Epidemiology

      Volume: 26 Issue: 9 Pages: 493-511

    • DOI

      10.2188/jea.JE20150268

    • NAID

      130005409018

    • ISSN
      0917-5040, 1349-9092
    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The structural origin of metabolic quantitative diversity2016

    • Author(s)
      Koshiba S, Motoike I, Kojima K, Hasegawa T, Shirota M, Saito T, Saigusa D, Danjoh I, Katsuoka F, Ogishima S, ... Yamamoto M.
    • Journal Title

      Sci Rep

      Volume: 6 Issue: 1 Pages: 31463-31463

    • DOI

      10.1038/srep31463

    • URL

      https://pure.teikyo.jp/en/publications/f23f66dd-859e-4088-8e53-de40d99cc561

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia.2016

    • Author(s)
      Mizuno S, Ogishima S, Nishigori H, Jamieson DG, Verspoor K, Tanaka H, Yaegashi N, Nakaya J.
    • Journal Title

      PLoS One

      Volume: 11(10) Issue: 10 Pages: e0162828-e0162828

    • DOI

      10.1371/journal.pone.0162828

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Development of biobank network in Japan2019

    • Author(s)
      Soichi Ogishima
    • Organizer
      AMED-GA4GH GEM Japan Workshop 2019 Sendai Symposium
    • Related Report
      2018 Annual Research Report
  • [Presentation] Integrated database "db TMM" for genomic prospective cohort study in Tohoku Medical Megabank Toward personalized healthcare2019

    • Author(s)
      荻島創一
    • Organizer
      生物試料の保管と活用に関するワークショップ
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] データ管理と共有・クラウドの利活用2019

    • Author(s)
      荻島創一
    • Organizer
      第2回バイオメディカルデータサイエンティスト養成集中講座
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Enabling genomic & phenotypic data sharing for the benefit of human health2018

    • Author(s)
      Soichi Ogishima
    • Organizer
      BioHackathon 2018
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] データベースはこれからの医療をこう変えてゆくか「データシェアリングの国外の動向と東北メディカル・メガバンク統合データベースdbTMMの取り組み」2018

    • Author(s)
      荻島創一
    • Organizer
      日本人類遺伝学会第63回大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] AMEDスポンサードセッション・バイオバンクの利活用促進と倫理的・法的・社会的課題(ELSI)「ゲノム医療実現推進のためのバイオバンク利活用促進に向けたバイオバンク・ネットワーク構 築と運用支援に関する研究開発」2018

    • Author(s)
      荻島創一
    • Organizer
      情報計算化学生物学会2018年大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 第2回オミックスを原理的なところから考える-「生命」と多様性を共存させる原理は?-2018

    • Author(s)
      荻島創一
    • Organizer
      情報計算化学生物学会2018年大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] バイオバンクのネットワーク化で何が変わるのか?「バイオバンクのネットワーク化と横断検索」2018

    • Author(s)
      荻島創一
    • Organizer
      第4回クリニカルバイオバンク学会シンポジウム
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 東北メディカル・メガバンク計画における統合データベースdbTMMの構築の現状と今後ー診療情報に基づくフェノタイピングによる追跡調査へ向けてー2018

    • Author(s)
      荻島創一
    • Organizer
      いわて東北メディカル・メガバンク機構講演会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Conduct the QOL survey using J-RARE - NANBYO Patients’ Data Platform led by patients2018

    • Author(s)
      Nishimura Y, Emoto S, Nishimura K, Iwasaki M, J-RARE patient organization groups, Yoshizawa G and Ogishima S
    • Organizer
      ECRD 2018
    • Related Report
      2018 Annual Research Report
  • [Presentation] バイオバンク横断検索のプロトタイプ開発 -バイオバンクの保管試料・情報の「見える化」とワンストップでの横断検索2018

    • Author(s)
      荻島創一
    • Organizer
      第3回バイオバンク連絡会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 個人情報保護法改正とゲノムデータの取扱い、国内外の動向2018

    • Author(s)
      荻島創一
    • Organizer
      バイオメディカルデータサイエンティスト養成集中講座
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] ビッグデータ・AI・ゲノム・創薬 セッション -AIや各種統計解析手法を用いたビッグデータ解析によるゲノム創薬の最前線2017

    • Author(s)
      荻島創一
    • Organizer
      第15回日本臨床腫瘍学会学術集会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 診療情報の利活用によるフェノタイピングとHuman Phenotype Ontology(HPO)2017

    • Author(s)
      荻島創一
    • Organizer
      第10回 Pharma AI Forum (PHAIFO)
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 前向きゲノムコホート研究へのNGSの貢献2017

    • Author(s)
      荻島創一
    • Organizer
      Kobe NGS Day
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 東北メディカル・メガバンク計画の進捗と統合データベースdbTMMの構築 -診療情報に基づくフェノタイピングによる追跡調査へ向けて-2017

    • Author(s)
      荻島創一
    • Organizer
      第80回徳島大学先端酵素学研究所糖尿病臨床・研究開発センター講演会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] ゲノム医療支援の人工知能の研究開発へ向けて:ゲノム医療とは?2017

    • Author(s)
      荻島創一
    • Organizer
      人工知能学会全国大会2017年度大会
    • Related Report
      2017 Research-status Report
  • [Presentation] 東北メディカル・メガバンク計画の進捗状況と日本のバイオバンクのこれから2017

    • Author(s)
      荻島創一
    • Organizer
      第3回クリニカルバイオバンク研究会
    • Related Report
      2017 Research-status Report
  • [Presentation] 東北メディカル・メガバンク 共同研究および分譲申請について2017

    • Author(s)
      荻島創一
    • Organizer
      第6回生命医薬情報学連合大会
    • Related Report
      2017 Research-status Report
  • [Presentation] Development of Tohoku Medical Megabank Integrated Database ”dbTMM” and Knowledge-Base "kbTMM"2017

    • Author(s)
      Soichi Ogishima
    • Organizer
      KI-Tohoku joint conference for international collaborations in Biobanking and Biochemistry (未来型医療拠点キックオフ 第二回カロリンスカ研究所・東北大学合同会議)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] ゲノム医療研究におけるPhenotyping2017

    • Author(s)
      荻島創一
    • Organizer
      第37回医療情報学連合大会
    • Related Report
      2017 Research-status Report
  • [Presentation] Network-based inference of signature genes of Alzheimer’s disease progression.2017

    • Author(s)
      Ogishima S, Tanaka H.
    • Organizer
      AROB Workshop on Artificial Life and Robotics in Busan
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] A method to associate all possible combinations of genetic and environmental factors using GxE landscape plot.2017

    • Author(s)
      Nagaie S, Ogishima S, Tanaka H.
    • Organizer
      AROB Workshop on Artificial Life and Robotics in Busan
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Minimum common data set in cross-biobank search across biobanks in Japan.2017

    • Author(s)
      Morita M, Hirata M, Ikeda S, Tomida S, Imoto S, Ogishima S.
    • Organizer
      Global Biobank Week 2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] A novel method of phenotype similarities of rare-disease patients using gene-pathway-phenotype relationships.2017

    • Author(s)
      Ogishima S, Nagaie S.
    • Organizer
      American Society of Human Genetics 2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] 未来型の個別化予防の実現に向けて - 統合・知識データベースの構築2016

    • Author(s)
      荻島創一
    • Organizer
      関西経済連合会 ビッグデータ利活用促進に向けた講演会(大阪府・大阪市)
    • Place of Presentation
      関西経済連合会(大阪府・大阪市)
    • Related Report
      2016 Research-status Report
    • Invited
  • [Book] ゲノム医療とゲノム創薬におけるビッグデータの活用「ヒトゲノム情報と創薬」2018

    • Author(s)
      荻島 創一
    • Total Pages
      4
    • Publisher
      癌と化学療法社
    • Related Report
      2018 Annual Research Report
  • [Book] ヒト疾患のデータベースとバイオバンク2017

    • Author(s)
      山本雅之, 荻島創一(編著)他共著
    • Total Pages
      229
    • Publisher
      羊土社
    • Related Report
      2017 Research-status Report
  • [Book] 改正個人情報保護法でゲノム研究はどう変わるか?-個人識別符号 ・ 要配慮情報としてのゲノムデータ2017

    • Author(s)
      清水佳奈, 山本奈津子, 川嶋実苗, 片山俊明, 荻島創一
    • Total Pages
      6
    • Publisher
      羊土社
    • Related Report
      2016 Research-status Report

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Published: 2016-04-21   Modified: 2020-03-30  

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