Transomics analysis with tensor decomposition based unsupervised feature extraction

• Project Area: Transomic Analysis of Metabolic Adaptation
• Project/Area Number: 20H04848
• 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): 2020-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2021: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2020: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: テンソル分解 / 変数選択 / マルチオミクス / 教師無し学習 / インシリコ創薬 / 腎臓がん / 前立腺がん / 教師なし学習 / マルチオミックスオミックス

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、トランスオミクスの研究を行うこと」である。

Outline of Annual Research Achievements

テンソル分解を用いた教師無し学習による変数選択法について複数の原著論文を刊行することができた。また以下の２つのパッケージをRのパッケージリポジト
リであるBioconductorで公開した。TDbasedUFE　https://bioconductor.org/packages/release/bioc/html/TDbasedUFE.html
TDbasedUFEad　https://bioconductor.org/packages/release/bioc/html/TDbasedUFEadv.html
これらのパッケージを用いて提案手法をより簡単に使えるようになった。Bioconductorは２０年以上の歴史がある世界的に有名なパッケージリポジトリであり、ここに複数のパッケージを公開することは厳正なレビューを通過しなくてはいけないこともあり非常に有意義なことである。また、このリポジトリに収録されることで世界中から多くのアクセスが見込まれ手法が広く使われて世界に広まることが期待できる。
これらのパッケージの内容の元になった論文を複数個、年度内に出版することにも成功しており、この点からも十分な成果が上がっていると考えることが可能である。また、これらに関係する発表も多数行っておりこれもまた成果に繋がっていると考えられるので十分な成果が上がっていると考えて問題ないと考えている。今後このパッケージが広く使われることで成果が世界的な物になっていくことが期待される。これとは別にINCOB2022で研究成果を発表し、パッケージの有効性が宣伝できた。また国内の研究会などでも研究成果を発表する機会に恵まれた。以上が今年度における成果の概要である。

Research Progress Status

令和3年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和3年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] Integrated Analysis of Tissue-Specific Gene Expression in Diabetes by Tensor Decomposition Can Identify Possible Associated Diseases (2022)
  • Author(s): Taguchi Y-H.、Turki Turki
  • Journal Title: Genes Volume: 13 Issue: 6 Pages: 1097-1097
  • DOI: 10.3390/genes13061097
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Handbook of Machine Learning Applications for Genomics (2022)
  • Author(s): Taguchi Y.-H.
  • Journal Title: Handbook of Machine Learning Applications for Genomics Volume: 1 Pages: 155-176
  • Peer Reviewed
• [Journal Article] Sincle Cell RNA-seq Analysis Using Tensor Decomposition and Principal Component Analysis Based Unsupervised Feature Extraction (2022)
  • Author(s): Taguchi Y.-H.
  • Journal Title: Handbook of Machine Learning Applications for Genomics Volume: 1 Pages: 155-176
  • DOI: 10.1007/978-981-16-9158-4_11
  • ISBN: 9789811691577, 9789811691584
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] In Silico Drug Discovery Using Tensor Decomposition Based Unsupervised Feature Extraction (2022)
  • Author(s): Taguchi Y.-H.
  • Journal Title: Handbook of Machine Learning Applications for Genomics Volume: 1 Pages: 101-120
  • DOI: 10.1007/978-981-16-9158-4_7
  • ISBN: 9789811691577, 9789811691584
  • Peer Reviewed
• [Journal Article] Multiomics Data Analysis of Cancers Using Tensor Decomposition and Principal Component Analysis Based Unsupervised Feature Extraction (2022)
  • Author(s): Taguchi Y.-H.
  • Journal Title: Handbook of Machine Learning Applications for Genomics Volume: 1 Pages: 1-17
  • DOI: 10.1007/978-981-16-9158-4_1
  • ISBN: 9789811691577, 9789811691584
  • Peer Reviewed
• [Journal Article] RNA m6A modification and microRNAs (2022)
  • Author(s): Taguchi Y.-H.
  • Journal Title: Handbook of Machine Learning Applications for Genomics Volume: 1 Pages: 169-180
  • DOI: 10.1016/b978-0-323-89774-7.00020-0
  • ISBN: 9780323897747
  • Peer Reviewed
• [Journal Article] Suppression of intrahepatic cholangiocarcinoma cell growth by <scp>SKI</scp> via upregulation of the <scp>CDK</scp> inhibitor p21 (2022)
  • Author(s): Kawamura E、Matsubara T、Daikoku A、et al.
  • Journal Title: FEBS Open Bio Volume: 12 Issue: 12 Pages: 2122-2135
  • DOI: 10.1002/2211-5463.13489
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Estimation of Metabolic Effects upon Cadmium Exposure during Pregnancy Using Tensor Decomposition (2022)
  • Author(s): Amakura Yuki、Taguchi Y-h.
  • Journal Title: Genes Volume: 13 Issue: 10 Pages: 1698-1698
  • DOI: 10.3390/genes13101698
  • Peer Reviewed / Open Access
• [Journal Article] Projection in genomic analysis: A theoretical basis to rationalize tensor decomposition and principal component analysis as feature selection tools (2022)
  • Author(s): Taguchi Y-h.、Turki Turki
  • Journal Title: PLOS ONE Volume: 17 Issue: 9 Pages: e0275472-e0275472
  • DOI: 10.1371/journal.pone.0275472
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Adapted tensor decomposition and PCA based unsupervised feature extraction select more biologically reasonable differentially expressed genes than conventional methods (2022)
  • Author(s): Taguchi Y-h.、Turki Turki
  • Journal Title: Scientific Reports Volume: 12 Issue: 1 Pages: 17438-17438
  • DOI: 10.1038/s41598-022-21474-z
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] microRNA Bioinformatics (2022)
  • Author(s): Taguchi Y-h.
  • Journal Title: Cells Volume: 11 Issue: 22 Pages: 3677-3677
  • DOI: 10.3390/cells11223677
  • Peer Reviewed / Open Access
• [Journal Article] A tensor decomposition-based integrated analysis applicable to multiple gene expression profiles without sample matching (2022)
  • Author(s): Taguchi Y-h.、Turki Turki
  • Journal Title: Scientific Reports Volume: 12 Issue: 1 Pages: 21242-21242
  • DOI: 10.1038/s41598-022-25524-4
  • Peer Reviewed / Open Access / Int'l Joint Research
• [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] 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mi RNA/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] 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 ～ (2020)
  • 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 ～ (2020)
  • 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
• [Presentation] Tensor decomposition and principal component analysis based unsupervised feature extraction with optimized standard deviation applied to gene expression, DNA methylation and histone modification (2022)
  • Author(s): Y-H. Taguchi , Ryo Ishibashi
  • Organizer: ISMB2022
  • Int'l Joint Research
• [Presentation] Identification of DNA loops in the Genome by Multi-Dimensional Scaling (2022)
  • Author(s): Ryo Ishibashi , Y-H. Taguchi
  • Organizer: ISMB2022
  • Int'l Joint Research
• [Presentation] Repurposing drugs for targeting 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): 田口善弘
  • 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: 保坂伸生 , 田口善弘
• [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, Turki Turki
  • 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)
• [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] 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] 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
• [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
• [Remarks] TDbasedUFE
  • URL: https://doi.org/doi:10.18129/B9.bioc.TDbasedUFE
• [Remarks] TDbasedUFEadv
  • URL: https://doi.org/doi:10.18129/B9.bioc.TDbasedUFEadv