Application of tensor decomposition based unsupervised feature extraction to histone modification analysis

• Project Area: Chromatin potential for gene regulation
• Project/Area Number: 19H05270
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Chuo University
• Principal Investigator: 田口 善弘 中央大学, 理工学部, 教授 (30206932)
• Project Period (FY): 2019-06-28 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000); Fiscal Year 2020: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000); Fiscal Year 2019: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
• Keywords: テンソル分解 / 教師無し学習 / インシリコ創薬 / 腎臓がん / 前立腺がん / 変数選択 / 教師なし学習 / ヒストン修飾

Outline of Research at the Start

研究目的に書いた通り、「『テンソル分解を用いた教師無し学習による変数選択法』を用いて、ヒストン修飾の研究を行うこと」である。

Outline of Annual Research Achievements

テンソル分解を用いることで臓器－薬物－遺伝子の関係をデータ駆動型で研究し、薬物の対象疾患が予測できることを示した。また、コロナウィルスの感染培養細胞の遺伝子発現プロファイルを解析することでコロナのインシリコ創薬が可能であることを示した。また、腎臓がんのmiRNAの発現プロファイルの解析で病態の変化に関係するmiRNAの検出が可能であることを示した。前立腺がんのマルチオミックス解析にテンソル分解の適用がゆうこうであることを示した。m6Aに関与する転写因子などの特定にも有効であることが分かった。

Research Progress Status

令和2年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和2年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] Exploring Common Therapeutic Targets for Neurodegenerative Disorders Using Transcriptome Study (2021)
  • Author(s): Dharshini S. Akila Parvathy、Jemimah Sherlyn、Taguchi Y. H.、Gromiha M. Michael
  • Journal Title: Frontiers in Genetics Volume: 12 Pages: 639160-639160
  • DOI: 10.3389/fgene.2021.639160
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] カーネルテンソル分解を用いた教師なし学習による変数選択法 ～ バイオインフォマティクスへの応用 ～ (2021)
  • Author(s): 田口 善弘
  • Journal Title: 信学技法 Volume: 120(395) Pages: 16-23
• [Journal Article] カーネルテンソル分解を用いた教師なし学習による変数選択法 ～ バイオインフォマティクスへの応用 ～ (2021)
  • Author(s): 田口 善弘
  • Journal Title: 情報処理学会研究報告 Volume: 2021-BIO-65(2) Pages: 1-9
• [Journal Article] 対面かオンラインか，それが問題だ (2020)
  • Author(s): 田口 善弘
  • Journal Title: Physics Education in University Volume: 26 Issue: 3 Pages: 115-115
  • DOI: 10.11316/peu.26.3_115
  • NAID: 130007955957
  • ISSN: 1340-993X, 2432-1710
  • Year and Date: 2020-11-15
• [Journal Article] Identifying suitable tools for variant detection and differential gene expression using RNA-seq data (2020)
  • Author(s): Dharshini S. Akila Parvathy、Taguchi Y.-H.、Gromiha M. Michael
  • Journal Title: Genomics Volume: 112 Issue: 3 Pages: 2166-2172
  • DOI: 10.1016/j.ygeno.2019.12.011
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Incremental Dilations Using CNN for Brain Tumor Classification (2020)
  • Author(s): Roy Sanjiban Sekhar、Rodrigues Nishant、Taguchi Y-h.
  • Journal Title: Applied Sciences Volume: 10 Issue: 14 Pages: 4915-4915
  • DOI: 10.3390/app10144915
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Universal Nature of Drug Treatment Responses in Drug-Tissue-Wide Model-Animal Experiments Using Tensor Decomposition-Based Unsupervised Feature Extraction (2020)
  • Author(s): Taguchi Yh.、Turki Turki
  • Journal Title: Frontiers in Genetics Volume: 11 Pages: 695-695
  • DOI: 10.3389/fgene.2020.00695
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A new advanced in silico drug discovery method for novel coronavirus (SARS-CoV-2) with tensor decomposition-based unsupervised feature extraction (2020)
  • Author(s): Taguchi Y-h.、Turki Turki
  • Journal Title: PLOS ONE Volume: 15 Issue: 9 Pages: 0238907-0238907
  • DOI: 10.1371/journal.pone.0238907
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of miRNA signatures for kidney renal clear cell carcinoma using the tensor-decomposition method (2020)
  • Author(s): Ng Ka-Lok、Taguchi Y.-H.
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 15149-15149
  • DOI: 10.1038/s41598-020-71997-6
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Developing a diagnostic method for latent tuberculosis infection using circulating miRNA (2020)
  • Author(s): Hashimoto Shoji、Zhao Hong、Hayakawa Michiyo、Nakajima Koichi、Taguchi Y-h、Murakami Yoshiki
  • Journal Title: Translational Medicine Communications Volume: 5 Issue: 1 Pages: 25-25
  • DOI: 10.1186/s41231-020-00078-7
  • Peer Reviewed / Open Access
• [Journal Article] Comprehensive analysis of liver and blood miRNA in precancerous conditions (2020)
  • Author(s): Umezu Tomohiro、Tsuneyama Koichi、Kanekura Kohsuke、Hayakawa Michiyo、Tanahashi Toshihito、Kawano Mitsuoki、Taguchi Y-h、Toyoda Hidenori、Tamori Akihiro、Kuroda Masahiko、Murakami Yoshiki
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 21766-21766
  • DOI: 10.1038/s41598-020-78500-1
  • Peer Reviewed / Open Access
• [Journal Article] Tensor-Decomposition-Based Unsupervised Feature Extraction Applied to Prostate Cancer Multiomics Data (2020)
  • Author(s): Taguchi Y-h.、Turki Turki
  • Journal Title: Genes Volume: 11 Issue: 12 Pages: 1493-1493
  • DOI: 10.3390/genes11121493
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of Transcription Factors, Biological Pathways, and Diseases as Mediated by N6-methyladenosine Using Tensor Decomposition-Based Unsupervised Feature Extraction (2020)
  • Author(s): Taguchi Y-h.、Dharshini S. Akila Parvathy、Gromiha M. Michael
  • Journal Title: Applied Sciences Volume: 11 Issue: 1 Pages: 213-213
  • DOI: 10.3390/app11010213
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 物理学者、機械学習を使う (2020)
  • Author(s): 田口善弘
  • Journal Title: 数理科学 Volume: 58(5) Pages: 63-63
• [Journal Article] テンソル分解に基づく教師なし学習による変数選択のRNAi 処理を行ったプラナリアのRNA-seq解析への適用 (2020)
  • Author(s): 田口善弘 , 鹿島誠
  • Journal Title: 情報処理学会研究報告 Volume: 2020-BIO-62(1) Pages: 1-4
• [Journal Article] Conjecturing human genes that are easy to be double strand breaks by tensor decomposition (2020)
  • Author(s): Nobuo Hosaka , Y-h. Taguchi
  • Journal Title: 情報処理学会研究報告 Volume: 2020-BIO-62(2) Pages: 1-6
• [Journal Article] Unsupervised feature extraction applied to bioinformatics (2020)
  • Author(s): Y-h. Taguchi
  • Journal Title: Research Outreach Volume: 115 Issue: 115 Pages: 154-157
  • DOI: 10.32907/ro-115-154157
  • Open Access
• [Journal Article] テンソル分解を用いた教師無し学習による変数選択法によるmiRNA/mRNA/プロテオームの統合解析 (2020)
  • Author(s): 田口 善弘
  • Journal Title: 情報処理学会研究報告 Volume: 2020-BIO-64(10) Pages: 1-5
• [Journal Article] Neurological Disorder Drug Discovery from Gene Expression with Tensor Decomposition (2020)
  • Author(s): Taguchi Y-h.、Turki Turki
  • Journal Title: Current Pharmaceutical Design Volume: 25 Issue: 43 Pages: 4589-4599
  • DOI: 10.2174/1381612825666191210160906
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Development of a novel anti-hepatitis B virus agent via Sp1 (2020)
  • Author(s): Hayakawa Michiyo、Umeyama Hideaki、Iwadate Mitsuo、Taguchi Y.-H.、Yano Yoshihiko、Honda Takashi、Itami-Matsumoto Saori、Kozuka Ritsuzo、Enomoto Masaru、Tamori Akihiro、Kawada Norifumi、Murakami Yoshiki
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 47-47
  • DOI: 10.1038/s41598-019-56842-9
  • Peer Reviewed / Open Access
• [Journal Article] SCGRNs: Novel supervised inference of single-cell gene regulatory networks of complex diseases (2020)
  • Author(s): Turki Turki、Taguchi Y-h.
  • Journal Title: Computers in Biology and Medicine Volume: 118 Pages: 103656-103656
  • DOI: 10.1016/j.compbiomed.2020.103656
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] テンソル分解を用いた教師無し学習による変数選択法の一細胞RNA-seq解析への応用 (2020)
  • Author(s): 田口 善弘
  • Journal Title: 信学技報 Volume: 119(360) Pages: 55-59
• [Journal Article] 機械学習による遺伝子情報の解析技術と 医薬品開発への応用 (2020)
  • Author(s): 田口 善弘
  • Journal Title: ファームステージ Volume: 19(11) Pages: 15-20
• [Journal Article] Sp1を標的としたHBVウィルスの新規阻害剤の探索 (2020)
  • Author(s): 早川 路代 , 梅山 秀明 , 岩舘 満雄 , 田口 善弘 , 村上 善基
  • Journal Title: 情報処理学会研究報告 Volume: 2020-BIO-61(1) Pages: 1-7
• [Journal Article] 『インストールいらずのLATEX入門』 (2019)
  • Author(s): 田口 善弘
  • Journal Title: Physics Education in University Volume: 25 Issue: 3 Pages: 147-148
  • DOI: 10.11316/peu.25.3_147
  • NAID: 130007761447
  • ISSN: 1340-993X, 2432-1710
  • Year and Date: 2019-11-15
• [Journal Article] Discovery of a Robust Gene Regulatory Network with a Complex Transcription Factor Network on Organ Cancer Cell-line RNA Sequence Data (2019)
  • Author(s): Kalbuaji Bharata、Taguchi Y-H.、Konagaya Akihiko
  • Journal Title: Chem-Bio Informatics Journal Volume: 19 Issue: 0 Pages: 32-55
  • DOI: 10.1273/cbij.19.32
  • NAID: 130007723654
  • ISSN: 1347-0442, 1347-6297
  • Year and Date: 2019-09-30
  • Peer Reviewed / Open Access
• [Journal Article] 機械学習のコモディティ化 (2019)
  • Author(s): 田口 善弘
  • Journal Title: Butsuri Volume: 74 Issue: 9 Pages: 659-660
  • DOI: 10.11316/butsuri.74.9_659
  • NAID: 130007807136
  • ISSN: 0029-0181, 2423-8872
  • Year and Date: 2019-09-05
  • Open Access
• [Journal Article] 『予備校のノリで学ぶ大学数学』 (2019)
  • Author(s): 田口 善弘
  • Journal Title: Physics Education in University Volume: 25 Issue: 2 Pages: 103-104
  • DOI: 10.11316/peu.25.2_103
  • NAID: 130007690075
  • ISSN: 1340-993X, 2432-1710
  • Year and Date: 2019-07-15
• [Journal Article] Tensor Decomposition-Based Unsupervised Feature Extraction Applied to Single-Cell Gene Expression Analysis (2019)
  • Author(s): Taguchi Y-h.、Turki Turki
  • Journal Title: Frontiers in Genetics Volume: 10 Pages: 864-864
  • DOI: 10.3389/fgene.2019.00864
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Investigating the energy crisis in Alzheimer disease using transcriptome study (2019)
  • Author(s): Dharshini S. Akila Parvathy、Taguchi Y.-h.、Gromiha M. Michael
  • Journal Title: Scientific Reports Volume: 9 Issue: 1 Pages: 18509-18509
  • DOI: 10.1038/s41598-019-54782-y
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] テンソル分解と主成分分解を用いた教師なし学習による社会性昆虫のカーストの脳の遺伝子発現プロファイルとDNAメチル化の解析 (2019)
  • Author(s): 田口善弘
  • Journal Title: 情報処理学会研究報告 Volume: 2019-BIO-58(61) Pages: 1-6
• [Journal Article] 生物学と物理学 (2019)
  • Author(s): 田口善弘
  • Journal Title: 窮理 Volume: 12 Pages: 1-9
• [Journal Article] テンソル分解に基づく教師なし学習による変数選択はMicroRNAトランスフェクションにより仲介されるmRNAの配列非特異的オフターゲット調節の普遍的性質を同定することができる (2019)
  • Author(s): 田口 善弘
  • Journal Title: 情報処理学会研究会報告 Volume: 2019-BIO-59(3) Pages: 1-7
• [Journal Article] テンソル分解を用いた教師なし学習による変数選択法のＴＣＧＡデータベースにおける卵巣がんデータのmicroRNA発現プロファイルとメチル化プロファイルへの適用 (2019)
  • Author(s): 田口 善弘 , 呉 家樂
  • Journal Title: 情報処理学会研究報告 Volume: 2019-BIO-60(2) Pages: 1-7
• [Journal Article] バイオインフォマティクスと倫理・社会 (2019)
  • Author(s): 田口 善弘
  • Journal Title: 信学技報 Volume: 119(329) Pages: 47-50
• [Presentation] Repurposing drugs for targetting SARS-Cov-2 (2020)
  • Author(s): Y-h. Taguchi
  • Organizer: IEEE ICBCB2020
  • Int'l Joint Research / Invited
• [Presentation] Application of Tensor Decomposition based Unsupervised Feature Extraction to Single Cell RNA-seq Data Analysis (2020)
  • Author(s): Y-h. Taguchi
  • Organizer: IEEE ICBCB2020
  • Int'l Joint Research / Invited
• [Presentation] Tensor decomposition based unsupervised Feature Extraction applied to in silico COVID-19 drug siscovery based upon analysis of gene expression profiles altered by SARS-CoV-2 infection (2020)
  • Author(s): Y-h. Taguchi
  • Organizer: 第九回生命医薬情報学連合大会(IIBMP2020)
• [Presentation] テンソル分解により二本鎖切断になりやすいヒト遺伝子の推定 (2020)
  • Author(s): 保坂伸生 , 田口善弘
  • Organizer: 第九回生命医薬情報学連合大会
• [Presentation] In silico drug discovery for COVID-19 using gene expression profiles of mouse infected by MHV and those of human cell lines infected by SARS-CoV-2 (2020)
  • Author(s): Y-h. Taguchi
  • Organizer: 7th Annual Congress of the European Society for Translational Medicine on Covid-19
  • Int'l Joint Research / Invited
• [Presentation] Selecting the genes related to COVID-19 with PCA-based unsupervised feature extraction (2020)
  • Author(s): Kota Fujisawa , Mamoru Shimo , Yoshihiro Taguchi , Shinya Ikematu , Ryota Miyata
  • Organizer: ＣＢＩ学会2020年会
• [Presentation] Identification of Transcription Factors, Biological Pathways, and Diseases as Mediated by N6-methyladenosine using Tensor Decomposition-Based Unsupervised Feature Extraction. (2020)
  • Author(s): Y-h. Taguchi , S Akila Parvathy Dharshini , M. Michael , Gromiha
  • Organizer: The 2nd International Symposium on Engineering and Technology (ISET 2020)
  • Int'l Joint Research
• [Presentation] テンソル分解を用いた教師無し学習による変数選択法を用いたCOVID-19治療薬の探索 (2020)
  • Author(s): 田口善弘 , Turki Turki
  • Organizer: IBIS2020
• [Presentation] Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivation (2020)
  • Author(s): Y-h. Taguchi
  • Organizer: The 19th International Conference on Bioinformatics (InCoB 2020)
  • Int'l Joint Research
• [Presentation] テンソル分解を用いた教師無し学習による変数選択法を用いたCOVID-19治療薬のリポジショニング (2020)
  • Author(s): 田口善弘 , Turki Turki
  • Organizer: 第43回日本分子生物学会年会
• [Presentation] テンソル分解を用いた教師なし学習による変数選択法を用いたゲノムデータ解析 (2020)
  • Author(s): 田口善弘
  • Organizer: イノベーションジャパン
• [Presentation] Principal Component Analysis, Tensor Decomposition, and Kernel Tensor Decomposition Based Unsupervised Feature Extraction Applied to Bioinformatics (2020)
  • Author(s): Y-h. Taguchi
  • Organizer: 2020 International Symposium on Automation, Information and Computing
  • Int'l Joint Research / Invited
• [Presentation] Application of tensor decomposition based unsupervised feature extraction to multi- omics data set (2019)
  • Author(s): Y-h. Taguchi
  • Organizer: BioInfOMICS2019
  • Int'l Joint Research / Invited
• [Presentation] Tensor decomposition based unsupervised feature extraction applied to bioinformatics (2019)
  • Author(s): Y-h. Taguchi
  • Organizer: PreMed'19
  • Int'l Joint Research / Invited
• [Presentation] テンソル分解を用いた教師無し学習による変数選択のマルチオミックスデータ解析への応用 (2019)
  • Author(s): 田口善弘
  • Organizer: 第４２回日本分子生物学会年会 2019年12月3日 日本分子生物学会
• [Presentation] Tensor decomposition based unsupervised feature extraction applied to drug discovery from gene expression analysis (2019)
  • Author(s): Y-h. Taguchi
  • Organizer: The 5th IITM - Tokyo Tech Joint Symposium titled "Current trends in Bioinformatics: Big data analysis, machine learning and drug design"
  • Int'l Joint Research / Invited
• [Book] 生命はデジタルでできている 情報から見た新しい生命像 (2020)
  • Author(s): 田口 善弘
  • Total Pages: 224
  • Publisher: 講談社
  • ISBN: 4065195977
• [Book] Regulatory microRNA (2020)
  • Author(s): 田口 善弘 , 王 秀瑛
  • Total Pages: 348
  • Publisher: MDPI
  • ISBN: 9783038977681
• [Book] Unsupervised Feature Extraction Applied to Bioinformatics A PCA Based and TD Based Approach (2019)
  • Author(s): Y-h. Taguchi
  • Total Pages: 321
  • Publisher: Springer International
  • ISBN: 9783030224554