Transcription regulatory network atlas for functional ncRNA search

• Project/Area Number: 15K12139
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Life / Health / Medical informatics
• Research Institution: Nagoya University
• Principal Investigator: Shimamura Teppei 名古屋大学, 医学系研究科, 特任准教授 (00623943)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2017: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2016: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
• Keywords: バイオインフォマティクス / システム生物学 / 遺伝子ネットワーク / 発現制御 / 転写制御

Outline of Final Research Achievements

In this research project, the purpose is to derive a probabilistic model describing the dynamics in which the regulatory relationship between the transcriptional regulatory factor and its target gene group is changed depending on the modulator from observed expression data and to identify functional ncRNAs controlling the transcriptional activity of various transcriptional regulators. As a result of applying the proposed method to simulation data and actual data, the following results were obtained. (A) Discovery of noncoding RNA that controls the oncogene MYC, and (B) development of a large-scale analysis pipeline for the comprehensive search of modulator factors, and construction of a transcriptional regulatory network atlas.

Research Products

• [Journal Article] Identification of Cardiomyocyte-Fated Progenitors from Human-Induced Pluripotent Stem Cells Marked with CD82 (2018)
  • Author(s): Takeda Masafumi、Kanki Yasuharu、Masumoto Hidetoshi、Funakoshi Shunsuke、Hatani Takeshi、Fukushima Hiroyuki、Izumi-Taguchi Akashi、Matsui Yusuke、Shimamura Teppei、Yoshida Yoshinori、Yamashita Jun K.
  • Journal Title: Cell Reports Volume: 22 Issue: 2 Pages: 546-556
  • DOI: 10.1016/j.celrep.2017.12.057
  • NAID: 120006460050
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Integrated Molecular Characterization of the Lethal Pediatric Cancer Pancreatoblastoma (2018)
  • Author(s): Isobe T, Seki M, Yoshida K, Sekiguchi M, Shiozawa Y, Shiraishi Y,..., Kataoka K, Sato Y, Kawai T, Chiba K, Tanaka H, Shimamura T, Kato M, Iguchi A, Hama A, Taguchi T, Akiyama M, Fujimura J, Inoue A, Ito T, Deguchi T, Kiyotani C, Iehara T, Hosoi H, Oka A, Sanada M, Tanaka Y, Hata K, Miyano S, Ogawa S, Takita J
  • Journal Title: Cancer Res Volume: 78(4) Issue: 4 Pages: 865-876
  • DOI: 10.1158/0008-5472.can-17-2581
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks (2018)
  • Author(s): Park H, Shimamura T, Imoto S, Miyano S
  • Journal Title: J Comput Biol Volume: 25(2) Issue: 2 Pages: 130-145
  • DOI: 10.1089/cmb.2017.0120
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] GIMLET: Identifying biological modulators in context-specific gene regulation using local energy statistics (2017)
  • Author(s): Shimamura Teppei, Matsui Yusuke, Kajino Taisuke, Takahashi Takashi, Miyano Satoru
  • Journal Title: Proceedings of CIBB2017 Volume: 1 Pages: 1-6
  • Peer Reviewed
• [Journal Article] Tumor subclonal progression model for cancer hallmark acquisition (2017)
  • Author(s): Matsui Yusuke, Miyano Satoru, Shimamura Teppei
  • Journal Title: Proceedings of CIBB2017 Volume: 1 Pages: 1-6
  • Peer Reviewed
• [Journal Article] phyC: Clustering cancer evolutionary trees. (2017)
  • Author(s): Matsui Y, Niida A, Uchi R, Mimori K, Miyano S, Shimamura T:
  • Journal Title: PLoS Comput Biol. Volume: 13(5) Issue: 5 Pages: 1005509-1005509
  • DOI: 10.1371/journal.pcbi.1005509
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] ER Stress Signaling Promotes the Survival of Cancer “Persister Cells” Tolerant to EGFR Tyrosine Kinase Inhibitors (2017)
  • Author(s): Terai Hideki、Kitajima Shunsuke、Potter Danielle S.、Matsui Yusuke、et al.
  • Journal Title: Cancer Research Volume: 78 Issue: 4 Pages: 1044-1057
  • DOI: 10.1158/0008-5472.can-17-1904
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Long Noncoding RNA JHDM1D-AS1 Promotes Tumor Growth by Regulating Angiogenesis in Response to Nutrient Starvation (2017)
  • Author(s): Kondo A, Nonaka A, Shimamura T, Yamamoto S, Yoshida T, Kodama T, Aburatani H, Osawa T
  • Journal Title: Molecular and Cellular Biology Volume: 37 Issue: 18
  • DOI: 10.1128/mcb.00125-17
  • Peer Reviewed / Open Access
• [Journal Article] Recurrent SPI1 (PU.1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia. (2017)
  • Author(s): Seki M, Kimura S, Isobe T, Yoshida K, (13 authors), Masuda K, Kawamoto H, Ohki K, Kato M, Arakawa Y, Koh K, Hanada R, Moritake H, Akiyama M, Kobayashi R, Deguchi T, Hashii Y, Imamura T, Sato A, Kiyokawa N, Oka A, Hayashi Y, Takagi M, Manabe A, Ohara A, Horibe K, Sanada M, Iwama A, Mano H, Miyano S, Ogawa S, Takita J
  • Journal Title: Nature Genetics Volume: 49 Issue: 8 Pages: 1274-1281
  • DOI: 10.1038/ng.3900
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] PRC2-Mediated Transcriptomic Alterations at the Embryonic Stage Govern Tumorigenesis and Clinical Outcome in MYCN-Driven Neuroblastoma (2017)
  • Author(s): 2.Tsubota S, Kishida S, Shimamura T, Ohira M, Yamashita S, Cao D, Kiyonari S, Ushijima T, Kadomatsu K.
  • Journal Title: Cancer Res. Volume: 77 Issue: 19 Pages: 5259-5271
  • DOI: 10.1158/0008-5472.can-16-3144
  • Peer Reviewed
• [Journal Article] High-resolution copy number variation analysis of schizophrenia in Japan. (2017)
  • Author(s): Kushima I, Aleksic B, Nakatochi M, Shimamura T, Shiino T, Yoshimi A, Kimura H, Takasaki Y, Wang C, Xing J, Ishizuka K, Oya-Ito T, Nakamura Y, Arioka Y, Maeda T, Yamamoto M, Yoshida M, Noma H, Hamada S, Morikawa M, Uno Y, Okada T, Iidaka T, Iritani S, Yamamoto T,
  • Journal Title: Molecular Psychiatry Volume: 22 Issue: 3 Pages: 430-440
  • DOI: 10.1038/mp.2016.88
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Extracellular Acidic pH Activates the Sterol Regulatory Element-binding Protein 2 to Promote Tumor Progression (2017)
  • Author(s): Kondo A, Yamamoto S, Nakaki R, Shimamura T, Hamakubo T, Sakai J, Kodama T, Yoshida T, Aburatani H and Osawa T
  • Journal Title: Cell Reports Volume: 18 Issue: 9 Pages: 2228-2242
  • DOI: 10.1016/j.celrep.2017.02.006
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Dynamically and epigenetically coordinated GATA/ETS/SOX transcription is indispensable for endothelial cell differentiation (2017)
  • Author(s): Kanki Y, Nakaki R, Shimamura T, Matsunaga T, Yamamizu K, Katayama S, Suehiro JI, Osawa T, Aburatani H, Kodama T, Wada Y, Yamashita JK, Minami T.
  • Journal Title: Nucleic Acids Research Volume: 印刷中 Issue: 8 Pages: 4344-4358
  • DOI: 10.1093/nar/gkx159
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Detection of differential distributions of methylation patterns (2016)
  • Author(s): Matsui Y, Mizuta M, Miyano S, Shimamura T
  • Journal Title: Bioinformatics Volume: 印刷中 Issue: 15 Pages: 1-8
  • DOI: 10.1093/bioinformatics/btw138
  • Peer Reviewed / Open Access
• [Journal Article] Aberrant Methylation of FOXE1 Contributes to a Poor Prognosis for Patients with Colorectal Cancer. (2016)
  • Author(s): Sugimachi K, Matsumura T, Shimamura T, Hirata H, Uchi R, Ueda M, Sakimura S, Iguchi T, Eguchi H, Masuda T, Morita K, Takenaka K, Maehara Y, Mori M, Mimori K.
  • Journal Title: Ann Surg Oncol. Volume: 23(12) Issue: 12 Pages: 3948-3955
  • DOI: 10.1245/s10434-016-5289-x
  • Peer Reviewed / Open Access
• [Journal Article] NECAB3 Promotes Activation of Hypoxia-inducible factor-1 during Normoxia and Enhances Tumourigenicity of Cancer Cells (2016)
  • Author(s): 1.Nakaoka HJ, Hara T, Yoshino S, Kanamori A, Matsui Y, Shimamura T, Sato H, Murakami Y, Seiki M, Sakamoto T
  • Journal Title: Sci Rep Volume: 6 Issue: 1 Pages: 22784-22784
  • DOI: 10.1038/srep22784
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution. (2016)
  • Author(s): R. Uchi (他40名, 山本36番目)
  • Journal Title: PLoS Genetics Volume: 12 Issue: 2 Pages: 1-24
  • DOI: 10.1371/journal.pgen.1005778
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Genomic Landscape of Esophageal Squamous Cell Carcinoma in a Japanese Population. (2016)
  • Author(s): G. Sawada (他43名, 山本21番目)
  • Journal Title: Gastroenterology Volume: 150 Issue: 5 Pages: 1171-1182
  • DOI: 10.1053/j.gastro.2016.01.035
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma (2015)
  • Author(s): Sawada G, Niida A, Hirata H, Komatsu H, Uchi R, Shimamura T, Takahashi Y, Kurashige J, Matsumura T, Ueo H, Takano Y, Ueda M, Sakimura S, Shinden Y, Eguchi H, Sudo T, Sugimachi K, Yamasaki M, Tanaka F, Tachimori Y, Kajiyama Y, Natsugoe S, Fujita H, Tanaka Y, Calin G, Miyano S, Doki Y, Mori M, Mimori K
  • Journal Title: PLoS One Volume: 10(10) Issue: 10 Pages: e0139808-e0139808
  • DOI: 10.1371/journal.pone.0139808
  • Peer Reviewed / Open Access
• [Journal Article] Integrated molecular analysis of adult T cell leukemia/lymphoma. (2015)
  • Author(s): Kataoka K, Nagata Y, Kitanaka A, Shiraishi Y, Shimamura T, Yasunaga J, Totoki Y, Chiba K, Sato-Otsubo A, Nagae G, et al.
  • Journal Title: Nat Genet. Volume: 47(11) Issue: 11 Pages: 1304-15
  • DOI: 10.1038/ng.3415
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models (2015)
  • Author(s): Hasegawa T, Niida A, Mori T, Shimamura T, Yamaguchi R, Miyano S, Akutsu T, Imoto S
  • Journal Title: Computational Statistics & Data Analysis Volume: 94 Pages: 63-74
  • DOI: 10.1016/j.csda.2015.08.003
  • Peer Reviewed
• [Journal Article] Elevated β-catenin pathway as a novel target for patients with resistance to EGF receptor targeting drugs (2015)
  • Author(s): Nakata A, Yoshida R, Yamaguchi R, Yamauchi M, Tamada Y, Fujita A, Shimamura T, Imoto S, Higuchi T, Nomura M, Kimura T, Nokihara H, Higashiyama M, Kondoh K, Nishihara H, Tojo A, Yano S, Miyano S, Gotoh N
  • Journal Title: Scientific Report Volume: 5 Issue: 1 Pages: 13076-13076
  • DOI: 10.1038/srep13076
  • NAID: 120005764206
  • Peer Reviewed / Open Access
• [Journal Article] Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. (2015)
  • Author(s): Seki M, Nishimura R, Yoshida K, Shimamura T, Shiraishi Y, Sato Y, Kato M, Chiba K, Tanaka H, Hoshino N, Nagae G, Shiozawa Y, Okuno Y, Hosoi H, Tanaka Y, Okita H, Miyachi M, Souzaki R, Taguchi T, Koh K, Hanada R, Kato K, Nomura Y, Akiyama M, Oka A, Igarashi T, Miyano S, Aburatani H, Hayashi Y, Ogawa S, Takita J.
  • Journal Title: Nat Commun. Volume: 6 Issue: 1 Pages: 7557-7557
  • DOI: 10.1038/ncomms8557
  • NAID: 120005623266
  • Peer Reviewed / Open Access
• [Journal Article] Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks (2015)
  • Author(s): Hasegawa T, Mori T, Yamaguchi R, Shimamura T, Miyano S, Imoto S, Akutsu T.
  • Journal Title: BMC Systems Biology Volume: 9 Issue: 1 Pages: 14-14
  • DOI: 10.1186/s12918-015-0154-2
  • NAID: 120005749949
  • Peer Reviewed / Open Access
• [Journal Article] Mutational landscape and clonal architecture in grade II and III gliomas (2015)
  • Author(s): Suzuki H, Aoki K, Natsume A, Ogawa S. et al.
  • Journal Title: Nat Genet. Volume: 47 Issue: 5 Pages: 458-468
  • DOI: 10.1038/ng.3273
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] 生命科学におけるビッグデータ駆動型科学の実践と将来 (2017)
  • Author(s): 島村徹平
  • Organizer: 2017年度生命科学系学会合同年次大会
  • Invited
• [Presentation] Analysis of Big Data - Genome Data - (2016)
  • Author(s): 島村徹平
  • Organizer: 実世界データ循環学サマースクール2016
  • Place of Presentation: ハノイ工科大学（ベトナム、ハノイ）
  • Invited
• [Presentation] 局所距離相関に基づくモジュレーター因子の網羅的探索法 (2016)
  • Author(s): 島村徹平
  • Organizer: 2016年度統計関連学会連合大会
  • Place of Presentation: 金沢大学（石川県金沢市）
  • Invited
• [Presentation] マルチオミックス情報に基づくがんのモジュレーター因子の網羅的探索 (2016)
  • Author(s): 島村徹平
  • Organizer: 第5回生命医薬情報学連合大会
  • Place of Presentation: 東京国際交流館プラザ平成（東京都江東区）
  • Invited
• [Presentation] システム生物学的アプローチに基づくオミックス統合解析 (2016)
  • Author(s): 島村徹平
  • Organizer: 第３９回分子生物学会年会
  • Place of Presentation: パシフィコ横浜（神奈川県横浜市）
  • Invited
• [Presentation] Identifying biological modulators using local energy statistics (2016)
  • Author(s): Teppei Shimamura
  • Organizer: CMStatistics 2016 (ERCIM2016)
  • Place of Presentation: セビリア大学（スペイン、セビリア）
  • Int'l Joint Research
• [Presentation] がんの俯瞰的理解のための統合的統計モデリング (2015)
  • Author(s): 島村徹平
  • Organizer: 第38回日本分子生物学会年会
  • Place of Presentation: 神戸ポートアイランド（兵庫県神戸市）
  • Year and Date: 2015-12-02
  • Invited
• [Presentation] がん悪性化に寄与する発現制御調整因子のイン・シリコ探索 (2015)
  • Author(s): 島村徹平
  • Organizer: がんゲノムの情報と数理
  • Place of Presentation: 東京大学医科学研究所（東京都港区）
  • Year and Date: 2015-09-30
  • Invited
• [Presentation] Discovering modulators of gene regulation by local energy statistics (2015)
  • Author(s): Teppei Shimamura
  • Organizer: IFCS2015
  • Place of Presentation: ボローニャ大学（イタリア、ボローニャ）
  • Year and Date: 2015-07-07
  • Int'l Joint Research