Development of extensive analyses methods of tumor and cell differentiation related miRNA using

• Project/Area Number: 23300357
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Tumor diagnosis
• Research Institution: Chuo University
• Principal Investigator: TAGUCHI Y-h. 中央大学, 理工学部, 教授 (30206932)
• Co-Investigator(Kenkyū-buntansha): YASUDA Jun 東北大学, 東北メディカル・メガバンク機構, 教授 (00281684)
• Project Period (FY): 2011-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥22,100,000 (Direct Cost: ¥17,000,000、Indirect Cost: ¥5,100,000); Fiscal Year 2013: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2012: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2011: ¥11,960,000 (Direct Cost: ¥9,200,000、Indirect Cost: ¥2,760,000)
• Keywords: microRNA / promoter methylation / histone modificatiuon / gene expression / ヒストン修飾 / 精子形成 / プロモーターメチル化 / 細胞老化 / 前頭葉 / 側頭葉 / 橋 / 小脳 / miRNA / ES細胞 / 髄芽腫

Outline of Final Research Achievements

We proposed MiRaGE (MiRNA Ranking by Gene Expression) that infer miRNA inhibition of target mRNAs using mRNA expression profiles and demonstrated its abilities. Replacing gene expression with promoter methylation or histone modification, we found the miRNA-target-specific promoter methylation and histone modifications.

Research Products

• [Journal Article] Apparent microRNA-Target-specific Histone Modification in Mammalian Spermatogenesis (2015)
  • Author(s): Y-h. Taguchi
  • Journal Title: Evolutionary Bioinformatics Volume: 11:Suppl 1 Pages: 13-26
  • DOI: 10.4137/ebo.s21832
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Apparent microRNA-target-specific histone modification in mammalian spermatogenesis (2014)
  • Author(s): Y-h. Taguchi
  • Journal Title: IPSJ SIG Technical Report Volume: 2014-BIO-39(2) Pages: 1-2
  • Acknowledgement Compliant
• [Journal Article] MicroRNA-mediated regulation of target genes in several brain regions is correlated to both microRNA-targeting-specific promoter methylation and differential microRNA expression. (2013)
  • Author(s): Y-h. Taguchi
  • Journal Title: BioData mining Volume: 6 Issue: 1 Pages: 11-11
  • DOI: 10.1186/1756-0381-6-11
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Principal component analysis based feature extraction approach to identify circulating microRNA biomarkers (2013)
  • Author(s): Y-h. Taguchi, Yoshiki Murakami
  • Journal Title: PLoS ONE Volume: 8 Issue: 6 Pages: e66714-e66714
  • DOI: 10.1371/journal.pone.0066714
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Correlation between miRNA-targeted-gene promoter methylation and miRNA regulation of target genes - See more at: http://f1000research.com/articles/2-21/v3#sthash.46klJq6T.dpuf (2013)
  • Author(s): Y-h. Taguchi
  • Journal Title: F1000Research Volume: 2 Pages: 21-21
  • DOI: 10.12688/f1000research.2-21.v3
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Possible miRNA coreguｌation of target genes in brain regions by both differential miRNA expression and miRNA-targeting-specific promoter methylation (2013)
  • Author(s): Y-h. Taguchi
  • Journal Title: IPSJ SIG Technical Reports Volume: 2013-BIO-33 Pages: 1-6
• [Journal Article] Inference of Target Gene Regulation via miRNAs during Cell Senescence by Using the MiRaGE Server (2012)
  • Author(s): Y-h. Taguchi
  • Journal Title: Aging and Disease Volume: 3 Pages: 301-306
  • Peer Reviewed
• [Journal Article] Inference of Target Gene Regulation via miRNAs during Cell Senescence by Using the MiRaGE Server (2012)
  • Author(s): Y-h. Taguchi
  • Journal Title: Communications in Computer and Information Science Volume: 304 Pages: 441-446
  • DOI: 10.1007/978-3-642-31837-5_64
  • ISBN: 9783642318368, 9783642318375
  • Peer Reviewed
• [Journal Article] Competitive target gene regulation by promoter methylation and miRNA (2012)
  • Author(s): Y-h. Taguchi
  • Journal Title: IPSJ SIG Technical Reports Volume: 2012-BIO-31 Pages: 1-6
• [Journal Article] Comprehensive miRNA expression analysis in peripheral blood can diagnose liver disease. (2012)
  • Author(s): Murakami Y, Toyoda H, Tanahashi T, Tanaka J, KumadaT, Yoshioka Y, Kosaka N, OchiyaT, Taguchi YH.
  • Journal Title: PLoS ONE Volume: 7(10) Issue: 10 Pages: e48366-e48366
  • DOI: 10.1371/journal.pone.0048366
  • Peer Reviewed
• [Journal Article] Comprehensive miRNA expression analysis in peripheral blood can diagnose liver disease (2012)
  • Author(s): Yoshiki Murakami
  • Journal Title: IPSJ SIG Technical Reports Volume: 2012-BIO-32 Pages: 1-6
• [Journal Article] 発現データからmiRNAの働きを予測する (2012)
  • Author(s): 田口善弘
  • Journal Title: 実験医学 Volume: 30 Pages: 1327-1332
• [Journal Article] Inference of target gene regulation via miRNAs during cell senescence by MiRaGE Server (2012)
  • Author(s): Y-h.Taguchi
  • Journal Title: IPSJ SIG Technical Report Volume: 2012-BIO-28:3 Pages: 1-6
• [Journal Article] Search of miRNAs critical for medulloblastoma formationusing MiRaGE method (2011)
  • Author(s): Y-h.Taguchi, Jun Yasuda
  • Journal Title: IPSJ SIG Technical Report Volume: 2011-BIO-25:5 Pages: 1-6
• [Journal Article] MiRaGE : Inference of Gene Expression Regulation via MicroRNA Transfection II (2011)
  • Author(s): Y-h.Taguchi, Jun Yasuda
  • Journal Title: Lecture Notes in Computer Science Volume: 6840 Pages: 129-135
  • DOI: 10.1007/978-3-642-24553-4_19
  • ISBN: 9783642245527, 9783642245534
  • Peer Reviewed
• [Journal Article] Inference of Gene Regulation via miRNAs During ES Cell Differentiation Using MiRaGE Method (2011)
  • Author(s): M.Yoshizawa, Y-h.Taguchi, J.Yasuda
  • Journal Title: Int.J.Mol.Sci. Volume: 12 Issue: 12 Pages: 9265-9276
  • DOI: 10.3390/ijms12129265
  • Peer Reviewed
• [Journal Article] Gene expression regulation during differentiation from murine ES cells due to microRNA (2011)
  • Author(s): M.Yoshizawa, Y-h.Taguchi
  • Journal Title: IPSJ SIG Technical Report Volume: 2011-BIO-25:38 Pages: 1-2
• [Presentation] Apparent microRNA-target-specific histone modification in mammalian spermatogenesis (2014)
  • Author(s): Y-h. Taguchi
  • Organizer: SIGBIO39
  • Place of Presentation: Osaka, Japan
  • Year and Date: 2014-09-12
• [Presentation] Possible miRNA Coregulation of Target Genes in Brain Regions by Both Differential miRNA Expression and miRNA-Targeting-Specific Promoter Methylation (2013)
  • Author(s): Y-h. Taguchi
  • Organizer: ICIC2013
  • Place of Presentation: Nanning, China
  • Year and Date: 2013-07-28 – 2013-07-31
• [Presentation] Gene expression regulation during differentiation from murine ES cells due to microRNA (2012)
  • Author(s): M.Yoshizawa, Y-h.Taguchi
  • Organizer: CBRC2011
  • Place of Presentation: 生命情報工学研究センター
  • Year and Date: 2012-01-24
• [Presentation] Inference of Target Gene Regulation via miRNAs during Cell Senescence by Using the MiRaGE Server (2012)
  • Author(s): Y-h. Taguchi
  • Organizer: ICIC2012
  • Place of Presentation: Huangshan, China
• [Presentation] Comprehensive miRNA expression analysis in peripheral blood can diagnose liver disease (2012)
  • Author(s): Y-h. Taguchi
  • Organizer: 第３２回バイオ情報学研究会
  • Place of Presentation: 京都大学
• [Presentation] MiRaGEサーバを用いた老化関連miRNAの標的遺伝子の発現制御予測 (2012)
  • Author(s): 田口善弘
  • Organizer: Biotech2012
  • Place of Presentation: 東京ビッグサイト
• [Presentation] Gene expression regulation during differentiation from murine ES cells due to microRNA (2011)
  • Author(s): M.Yoshizawa, Y-h.Taguchi
  • Organizer: 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops
  • Place of Presentation: Marriott Atlanta Marquis
  • Year and Date: 2011-11-12
• [Presentation] An application to infer the important miRNAs in a biological process : MiRaGE method (2011)
  • Author(s): Y-h.Taguchi, Jun Yasuda
  • Organizer: Cell Symposia : Regulatory RNA
  • Place of Presentation: Wyndham Hotel
  • Year and Date: 2011-11-10
• [Presentation] Inference of gene expression regulation by miRNA using MiRaGE method (2011)
  • Author(s): Y-h.Taguchi, J.Yasuda
  • Organizer: IIT Madras-Tokyo Tech joint Workshop on Bioinformatics and Large Scale Data Analysis
  • Place of Presentation: IIT Madras(invited)
  • Year and Date: 2011-07-16
• [Presentation] MiRaGE法を用いたmiRNAによる遺伝子発現制御 (2011)
  • Author(s): Y-h.Taguchi, J.Yasuda
  • Organizer: バイオテクノロジー国際会議
  • Place of Presentation: 東京ビッグサイト
  • Year and Date: 2011-06-30
• [Presentation] Inference of miRNA transfection via gene expression with MiRaGE method (2011)
  • Author(s): Y-h.Taguchi, Jun Yasuda
  • Organizer: RNA2011
  • Place of Presentation: 京都国際会館
  • Year and Date: 2011-06-14
• [Presentation] Possible miRNA coreguｌation of target genes in brain regions by both differential miRNA expression and miRNA-targeting-specific promoter methylation
  • Author(s): Y-h. Taguchi
  • Organizer: 第３３回バイオ情報学研究会
  • Place of Presentation: 東北大学
• [Presentation] Competitive target gene regulation by promoter methylation and miRNA
  • Author(s): Y-h. Taguchi
  • Organizer: 第３１回バイオ情報学研究会
  • Place of Presentation: タワーホール船堀
• [Remarks] MiRNA Ranking by Gene Expression
  • URL: http://www.bioconductor.org/packages/release/bioc/html/MiRaGE.html
• [Remarks] gene target table of miRNA used for MiRaGE package
  • URL: http://www.bioconductor.org/packages/release/data/experiment/html/miRNATarget.html
• [Remarks]
  • URL: http://www.granular.com/MiRaGE/