変数選択安定性を重視した変数選択を用いたオミックス疾患バイオマーカー探索

• Project Area: Initiative for High-Dimensional Data-Driven Science through Deepening of Sparse Modeling
• Project/Area Number: 26120528
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Complex systems
• Research Institution: Chuo University
• Principal Investigator: 田口 善弘 中央大学, 理工学部, 教授 (30206932)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000); Fiscal Year 2015: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000); Fiscal Year 2014: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
• Keywords: 心的外傷後ストレス障害 / 筋萎縮性側索硬化症 / 世代間エピジェネティックス / mRNA-miRNA相互作用 / 出芽酵母の細胞分裂周期遺伝子 / 心筋細胞の成熟プロセス遺伝子 / 非小細胞肺がんのエピジェネティック療法 / デング出血熱 / マイクロRNA / 普遍疾患バイオマーカー / 遺伝子発現解析 / 自己免疫疾患 / 非小細胞肺がん

Outline of Annual Research Achievements

主成分分析を用いた教師なし学習による変数選択法をいろいろな問題に適用した。
1) PTSD(心的外傷後ストレス障害)由来の心臓病原因遺伝子の解析：miRNAとmRNAの心臓の発現プロファイルの解析からFABP3を原因遺伝子として同定し、インシリコ創薬で治療薬の提案を行った。２）ALS（筋萎縮性側索硬化症）の原因遺伝子の解析：ALSの患者の皮膚の培養細胞の遺伝子発現プロファイルの統合解析から原因遺伝子を同定し、インシリコ創薬で治療薬の提案を行った。３）世代間エピジェネティックスの原因遺伝子の推定：エピジェネティックマーカーの遺伝機構の解明のため、胎児の遺伝子発現プロファイル、プロモーターメチル化の統合解析から、原因遺伝子の推定を行った。４）複数のがんのmRNA-miRNA相互作用の推定：mRNA/miRNA発現プロファイルの統合解析から、複数種のがんに対して。統一的な基準から相互作用しているペアの道程を行った。５）出芽酵母の細胞分裂周期遺伝子の推定：出芽酵母の細胞分裂プロセスの遺伝子発現プロファイルを解析して細胞分裂プロセスに寄与する遺伝子を推定し、従来法よりよい結果を得た。６）心筋細胞の成熟プロセス遺伝子の同定：心筋細胞成熟プロセスにおける遺伝子発現プロファイルをヒトとマウスで比較し、重要遺伝子を推定した。７）非小細胞肺がんのエピジェネティック療法の標的遺伝子の推定：非小細胞肺がんのリプログラミング実験の遺伝子発現ポロファイルとプロモーターメチル化プロファイルを統合解析し、SFRP1をエピジェネティック療法の標的遺伝子として同定した。８）恐怖記憶療法標的遺伝子：ヒストン脱アセチル化阻害剤によつ恐怖記憶消去加速の機構を複数の阻害剤の効果の統合解析から解明した。９）デング熱：デング出血熱の原因遺伝子の推定を複数の患者の血液遺伝子発現プロファイルの解析から行った。

Research Progress Status

27年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

27年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] MicroRNA expression in hepatocellular carcinoma after the eradication of chronic hepatitis virus C infection using interferon therapy (2016)
  • Author(s): Tamori, A
  • Journal Title: Hepatology Res Volume: 46 Issue: 3 Pages: 26-35
  • DOI: 10.1111/hepr.12518
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Identification of More Feasible MicroRNA-mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction (2016)
  • Author(s): YH Taguchi
  • Journal Title: International Journal of Molecular Sciences Volume: 17(5) Issue: 5 Pages: 696-696
  • DOI: 10.3390/ijms17050696
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Principal component analysis based unsupervised feature extraction applied to budding yeast temporally periodic gene expression (2016)
  • Author(s): YH Taguchi
  • Journal Title: Biodata Mining Volume: 9 Issue: 1 Pages: 22-22
  • DOI: 10.1186/s13040-016-0101-9
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Comparative Gene Expression Analysis of Mouse and Human Cardiac Maturation (2016)
  • Author(s): Hideki Uosaki, Y.H Taguchi
  • Journal Title: Genomics Proteomics & Bioinformatics Volume: 14 Issue: 4 Pages: 207-215
  • DOI: 10.1016/j.gpb.2016.04.004
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] SFRP1 is a possible candidate for epigenetic therapy in non-small cell lung cancer (2016)
  • Author(s): YH Taguchi, Mitsuo Iwadate, Hideaki Umeyama
  • Journal Title: BMC Medical Genomics Volume: 9(Suppl 1) Issue: S1 Pages: 28-28
  • DOI: 10.1186/s12920-016-0196-3
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Principal component analysis based unsupervised feature extraction applied to publicly available gene expression profiles provides new insights into the mechanisms of action of histone deacetylase inhibitors (2016)
  • Author(s): YH. Taguchi
  • Journal Title: Neuroepigenetics Volume: 8 Pages: 1-18
  • DOI: 10.1016/j.nepig.2016.10.001
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Principal Components Analysis Based Unsupervised Feature Extraction Applied to Gene Expression Analysis of Blood from Dengue Haemorrhagic Fever Patients (2016)
  • Author(s): YH. Taguchi
  • Journal Title: Scientific reports Volume: 7 Issue: 1 Pages: 44016-44016
  • DOI: 10.1038/srep44016
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Exploring effective multiplicity in multichannel functional near-infrared spectroscopy using eigenvalues of correlation matrices. (2015)
  • Author(s): Minako Uga, Ippeita Dan, Haruka Dan, Yasushi Kyutoku, Y-h Taguchi, Eiju Watanabe
  • Journal Title: Neurophotonics Volume: 2 Issue: 1 Pages: 015002-015002
  • DOI: 10.1117/1.nph.2.1.015002
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [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] Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease (2015)
  • Author(s): YH Taguchi, M Iwadate, H Umeyama
  • Journal Title: BMC bioinformatics Volume: 16(1) Issue: 1 Pages: 139-139
  • DOI: 10.1186/s12859-015-0574-4
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Heuristic principal component analysis-based unsupervised feature extraction and its application to gene expression analysis of amyotrophic lateral sclerosis data sets (2015)
  • Author(s): YH Taguchi, Mitsuo Iwadate, Hideaki Umeyama
  • Journal Title: 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology Volume: 0 Pages: 1-10
  • DOI: 10.1109/cibcb.2015.7300274
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] <i>In silico</i> Spleen Tyrosine Kinase Inhibitor Screening by ChooseLD (2015)
  • Author(s): H Umeyama, M Iwadate, YH Taguchi
  • Journal Title: IPSJ Transactions on Bioinformatics Volume: 8 Issue: 0 Pages: 14-20
  • DOI: 10.2197/ipsjtbio.8.14
  • NAID: 130005094264
  • ISSN: 1882-6679
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Comprehensive analysis of transcriptome and metabolome analysis in Intrahepatic Cholangiocarcinoma and Hepatocellular Carcinoma (2015)
  • Author(s): Murakami, Y
  • Journal Title: Scientific Reports Volume: 5 Issue: 1 Pages: 16294-16294
  • DOI: 10.1038/srep16294
  • NAID: 120005820886
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target (2015)
  • Author(s): Chiba S, Akiyama Y, Sekijima M.
  • Journal Title: Scientific Reports Volume: 5 Issue: 1 Pages: 1-13
  • DOI: 10.1038/srep17209
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of aberrant gene expression associated with aberrant promoter methylation in primordial germ cells between E13 and E16 rat F3 generation vinclozolin lineage (2015)
  • Author(s): Y-H. Taguchi
  • Journal Title: BMC Bioinformatics Volume: 16(Suppl 18) Issue: S18
  • DOI: 10.1186/1471-2105-16-s18-s16
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Subtype specific promoter methylation in glioblastoma (2014)
  • Author(s): Kiyohiko Sakamoto, Y-h Taguchi
  • Journal Title: IPSJ SIG Technical Report Volume: 2014-BIO-38(2) Pages: 1-2
  • Acknowledgement Compliant
• [Journal Article] Bioinformatic screening of autoimmune disease genes and protein structure prediction with FAMS for drug discovery (2014)
  • Author(s): Shigeharu Ishida, Hideaki Umeyama, Mitsuo Iwadate, Y-h. Taguchi
  • Journal Title: Protein Pept Lett Volume: 21(8) Issue: 8 Pages: 823-839
  • DOI: 10.2174/09298665113209990052
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Universal disease biomarker: can a fixed set of blood microRNAs diagnose multiple diseases? (2014)
  • Author(s): Y-h. Taguchi
  • Journal Title: BMC Research Notes Volume: 7(1) Issue: 1 Pages: 581-581
  • DOI: 10.1186/1756-0500-7-581
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray (2014)
  • Author(s): Yoshiki Murakami, Toshihito Tanahashi, Rina Okada, Hidenori Toyoda, Takashi Kumada, Masaru Enomoto, Akihiro Tamori, Norifumi Kawada, Y-H Taguchi, Takeshi Azuma
  • Journal Title: PLoS ONE Volume: 9(9) Issue: 12 Pages: e116434-e116434
  • DOI: 10.1371/journal.pone.0116434
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] FAMSとchooseLDを用いたインシリコ創薬パイプライン (2017)
  • Author(s): 田口善弘
  • Organizer: 第７回化粧品開発展
  • Place of Presentation: ビッグサイト
• [Presentation] microRNA-mRNA interaction identification in Wilms tumor using principal component analysis based unsupervised feature extraction (2016)
  • Author(s): Y-h. Taguchi
  • Organizer: 2016 IEEE 16th International Conference on Bioinformatics and Bioengineering
  • Place of Presentation: The Splendor Hotel Taichung
  • Year and Date: 2016-10-31
  • Int'l Joint Research
• [Presentation] Comprehensive analysis of transcriptome and metabolome analysis in Intrahepatic Cholangiocarcinoma and Hepatocellular Carcinoma (2016)
  • Author(s): Yoshiki Murakami, Shoji Kubo, Akihiro Tamori, Saori Itami, Etsushi Kawamura, Keiko Iwaisako, Kazuo Ikeda, Norifumi Kawada, Takahiro Ochiya and Y-H. Taguchi
  • 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
  • Year and Date: 2016-09-29
• [Presentation] FAMSとchooseLDを用いたインシリコ創薬パイプライン (2016)
  • Author(s): 田口善弘
  • Organizer: 第13回アカデミックフォーラム
  • Place of Presentation: ビッグサイト
  • Year and Date: 2016-05-11
• [Presentation] Principal component analysis based unsupervised feature extraction applied to various bioinformatic analyses (2015)
  • Author(s): Y-h. Taguchi
  • Organizer: 3rd IIT Madras ; Tokyo Tech Joint Symposium on "Algorithms and Applications of Bioinformatics"
  • Place of Presentation: IIT Madras
  • Year and Date: 2015-11-05
  • Int'l Joint Research
• [Presentation] Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease (2015)
  • Author(s): 田口善弘・岩舘満雄・梅山秀明
  • Organizer: 生命医薬情報学連合大会 2015年大会
  • Place of Presentation: 京都大学宇治キャンパスおうばくプラザ
  • Year and Date: 2015-10-29
• [Presentation] FAMSとchooseLDを用いたインシリコ創薬パイプライン (2015)
  • Author(s): 田口善弘
  • Organizer: BioJapan2015
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2015-10-14
• [Presentation] FAMSとchooseLDを用いたインシリコ創薬パイプライン (2015)
  • Author(s): 田口善弘・梅山秀明・岩舘満雄
  • Organizer: ライフサイエンスワールド2015/第12回アカデミックフォーラム
  • Place of Presentation: ビッグサイト
  • Year and Date: 2015-05-13
• [Presentation] Integrative Analysis of Gene Expression and Promoter Methylation during Reprogramming of a Non-Small-Cell Lung Cancer Cell Line Using Principal Component Analysis-Based Unsupervised Feature Extraction (2014)
  • Author(s): Y-h. Taguchi
  • Organizer: ICIC2014
  • Place of Presentation: 中国・太原市
  • Year and Date: 2014-08-03 – 2014-08-06