A big data approach to function prediction of metabolites by clustering of structural similarity networks

• 研究課題/領域番号: 17K00406
• 研究種目: 基盤研究(C)
• 配分区分: 基金
• 応募区分: 一般
• 研究分野: 生命・健康・医療情報学
• 研究機関: 奈良先端科学技術大学院大学
• 研究代表者: AMIN MD.ALTAFUL 奈良先端科学技術大学院大学, 先端科学技術研究科, 准教授 (30379531)
• 研究期間 (年度): 2017-04-01 – 2020-03-31
• 研究課題ステータス: 完了 (2019年度)
• 配分額: 3,250千円 (直接経費: 2,500千円、間接経費: 750千円); 2019年度: 780千円 (直接経費: 600千円、間接経費: 180千円); 2018年度: 780千円 (直接経費: 600千円、間接経費: 180千円); 2017年度: 1,690千円 (直接経費: 1,300千円、間接経費: 390千円)
• キーワード: Metabolomics / Metabolic Network / Network Clustering / Metabolite Activity / Big Data Biology / Algorithm / Systems Biology / Algorithms / Big data biology / Network clustering / Secondary metabolites

研究成果の概要

私たちは代謝物の活性を予測する手法を開発し、この手法を用いて1340種類の未知の代謝物の機能を予測することができた。またプロジェクトの一環として、単純グラフと2部グラフのクラスタリングのためのDPClusSBOというツールを開発した。このプロジェクトを中心に論文を多数発表していて、マレーシア、ブラジル、インドネシアの共同研究者もこのツールを使用している。将来的にはさらに広くこのツールが使用されることを期待していて、またツール自体も伝統医学の抗生物質の探索など応用範囲を広げていきたいと考えている。

研究成果の学術的意義や社会的意義

By utilizing our method we predicted the functions of 1340 unknown metabolites. As part of this project we developed a tool for clustering of simple and bipartite graphs which we have utilized in several other research works. This tool is a significant academic and social achievement.

研究成果

• [雑誌論文] Discovery of inflammatory bowel disease-associated miRNAs using a novel bipartite clustering approach (2020)
  • 著者名/発表者名: Altaf-Ul-Amin, M., Karim, M. B., Hu, P., Naoaki, O. N. O., & Kanaya, S.
  • 雑誌名: BMC Medical Genomics 巻: 13(3) 号: S3 ページ: 1-10
  • DOI: 10.1186/s12920-020-0660-y
• [雑誌論文] Graph cluster approach in identifying novel proteins and significant pathways involved in polycystic ovary syndrome (2020)
  • 著者名/発表者名: Afiqah-Aleng, N., Altaf-Ul-Amin, M., Kanaya, S., & Mohamed-Hussein, Z. A.
  • 雑誌名: Reproductive biomedicine online 巻: 40(2) 号: 2 ページ: 319-330
  • DOI: 10.1016/j.rbmo.2019.11.012
• [雑誌論文] BiClusO: A novel biclustering approach and its application to species-VOC relationship data (2019)
  • 著者名/発表者名: Mohammad Bozlul Karim, Ming Huang, Naoaki ONO, Shigehiko Kanaya, Md. Altaf-Ul Amin
  • 雑誌名: IEEE/ACM transactions on computational biology and bioinformatics 巻: 2019 号: 6 ページ: 1-12
  • DOI: 10.1109/tcbb.2019.2914901
• [雑誌論文] Implementation of BiClusO and its comparison with other biclustering algorithms (2019)
  • 著者名/発表者名: Mohammad Bozlul Karim, Shigehiko Kanaya, Md. Altaf-Ul-Amin
  • 雑誌名: Applied Network Science 巻: 4(1) ページ: 1-15
• [雑誌論文] [Special Issue for Honor Award dedicating to Prof Kimito Funatsu]Prediction of Metabolite Activities by Repetitive Clustering of the Structural Similarity Based Networks (2019)
  • 著者名/発表者名: Wakamatsu, N., Huang, M., Ono, N., Altaf-Ul-Amin, M., & Kanaya, S.
  • 雑誌名: Journal of Computer Aided Chemistry 巻: 20 号: 0 ページ: 76-83
  • DOI: 10.2751/jcac.20.76
  • NAID: 130007775607
  • ISSN: 1345-8647
• [雑誌論文] On the determination of important plants for ayurvedic formulas in Bangladesh using unsupervised machine learning approach (2019)
  • 著者名/発表者名: Hossain M. Mofazzal, M. S. A. Gazi, M. Mahbub, A. A. P. Sayed, S. Kanaya and M. Altaf-Ul-Amin
  • 雑誌名: Academia Journal of Medicinal Plants 巻: 7(2) ページ: 036-041
• [雑誌論文] An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease (2018)
  • 著者名/発表者名: Eguchi, R., Karim, M. B., Hu, P., Sato, T., Ono, N., Kanaya, S., & Altaf-Ul-Amin, M.
  • 雑誌名: BMC bioinformatics 巻: 19(1) 号: 1 ページ: 264-264
  • DOI: 10.1186/s12859-018-2251-x
  • 査読あり
• [雑誌論文] Metabolite-Content-Guided Prediction of Medicinal/Edible Prop-erties in Plants for Bioprospecting (2018)
  • 著者名/発表者名: Liu, K., Morita, A. H., Kanaya, S., & Atlaf-Ul-Amin, M
  • 雑誌名: Current Research in Complementary & Alternative Medicine 巻: CRCAM-130 号: 2 ページ: 2577-2201
  • DOI: 10.29011/2577-2201/100030
• [雑誌論文] データサイエンスから解明される世界の食用生物の多様性とヘルスケア (2018)
  • 著者名/発表者名: Watanabe, Satoshi, K. Y. O. Hoko, K. A. N. G. Liu, Ryohei Eguchi, Md Altaf-Ul-Amin, Aki MORITA, Minako OHASHI et al.
  • 雑誌名: 日本補完代替医療学会誌 巻: 15 号: 1 ページ: 37-60
  • DOI: 10.1625/jcam.15.37
  • NAID: 130006708552
  • ISSN: 1348-7922, 1348-7930
• [雑誌論文] Classification of lung adenocarcinoma transcriptome subtypes from pathological images using deep convolutional networks (2018)
  • 著者名/発表者名: 3.Antonio, V. A. A., Ono, N., Saito, A., Sato, T., Altaf-Ul-Amin, M., & Kanaya, S.
  • 雑誌名: International journal of computer assisted radiology and surgery 巻: 13(12) 号: 12 ページ: 1905-1913
  • DOI: 10.1007/s11548-018-1835-2
  • 査読あり / オープンアクセス
• [雑誌論文] Metabolite-Content-Guided Prediction of Medicinal/Edible Prop-erties in Plants for Bioprospecting (2018)
  • 著者名/発表者名: Liu, K., Morita, A. H., Kanaya, S., & Atlaf-Ul-Amin, M.
  • 雑誌名: Curr Res Complement Altern Med 巻: 130 ページ: 1-15
• [雑誌論文] Metabolomic Studies of Indonesian Jamu Medicines: Prediction of Jamu Efficacy and Identification of Important Metabolites (2017)
  • 著者名/発表者名: Sony Hartono Wijaya, Irmanida Batubara, Takaaki Nishioka, Md. Altaf-Ul-Amin, and Shigehiko Kanaya
  • 雑誌名: Molecular Informatics 巻: 36 号: 12 ページ: 1-16
  • DOI: 10.1002/minf.201700050
• [雑誌論文] [Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]Classification of Alkaloid Compounds Based on Subring Skeleton (SRS) Profiling: On Finding Relationship of Compounds with Metabolic Pathways (2017)
  • 著者名/発表者名: Eguchi, R., Ono, N., Horai, H., Amin, M. A. U., Hirai, A. M., Kawahara, J., ... & Kanaya, S.
  • 雑誌名: Journal of Computer Aided Chemistry 巻: 18 号: 0 ページ: 58-75
  • DOI: 10.2751/jcac.18.58
  • NAID: 130005877929
  • ISSN: 1345-8647
  • 査読あり / オープンアクセス
• [雑誌論文] [Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]DPClusOST: A Software Tool for General Purpose Graph Clustering (2017)
  • 著者名/発表者名: Mohammad Bozlul Karim, Nobutaka Wakamatsu and Md. Altaf-Ul-Amin
  • 雑誌名: Journal of Computer Aided Chemistry 巻: 18 号: 0 ページ: 76-93
  • DOI: 10.2751/jcac.18.76
  • NAID: 130005877930
  • ISSN: 1345-8647
• [学会発表] Applications of KNApSAcK Database and DPClus Algorithm: Plants to Metabolites to Target Proteins in the Context of Jamu Medicines and IBD Gene Prediction (2020)
  • 著者名/発表者名: Md. Altaf-Ul-Amin
  • 学会等名: Asian Regional Conference on Systems Biology
  • 国際学会
• [学会発表] Novel Method and Tool for Clustering of Simple and Bipartite Graphs: Applications in Ecology and Identification of Inflammatory Bowel Disease(IBD) Related Genes and miRNAs (2020)
  • 著者名/発表者名: Md. Altaf-Ul-Amin
  • 学会等名: University of south Australia, Adelaide
  • 招待講演
• [学会発表] Inter Disease Relations Based on Human Biomarkers by Network Analysis (2019)
  • 著者名/発表者名: Md. Altaf-Ul-Amin
  • 学会等名: IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)
  • 国際学会
• [学会発表] Discovery of inflammatory bowel disease-associated miRNAs using a novel bipartite clustering approach (2019)
  • 著者名/発表者名: Md. Altaf-Ul-Amin
  • 学会等名: International Conference on Genome Informatics (GIW 2019)
  • 国際学会
• [学会発表] Development of an Integrated System for Clustering of Simple and Bipartite Graphs and its Application to Different Types of Biological Data (2019)
  • 著者名/発表者名: Md. Altaf-Ul-Amin
  • 学会等名: University of Manitoba, Canada
  • 招待講演
• [学会発表] Applications of KNApSAcK Database and DPClus Algorithm: Plants to Metabolites to Target Proteins in the Context of Jamu Medicines and IBD Gene Prediction (2019)
  • 著者名/発表者名: Md. Altaf-Ul-Amin
  • 学会等名: ICBET 2019, Meiji University, Tokyo
  • 招待講演
• [学会発表] Introduction to Big Data Science Focusing Health Care and Ecology: A Case Study based on Indonesian Traditional Medicines (2019)
  • 著者名/発表者名: Md. Altaf-Ul-Amin
  • 学会等名: Big data: Linking Ecosystem, health and wellbeing, BUET, Dhaka, Bangladesh
  • 招待講演
• [学会発表] Data-Intensive Science of Jamu Medicines (2018)
  • 著者名/発表者名: Md. Altaf-Ul-Amin
  • 学会等名: Universidade Federal de São Paulo, Brazil
  • 招待講演
• [学会発表] Comparison of BiClusO with five different biclustering algorithms using biological and Synthetic data (2018)
  • 著者名/発表者名: Mohammand Bozlul Karim
  • 学会等名: 7th International Conference on Complex Networks and Their Applications, Cambridge, UK
• [学会発表] Prediction of Plant-Disease Relations Based on Unani Formulas by Network Analysis (2018)
  • 著者名/発表者名: Shaikh Farhad Hossain
  • 学会等名: 18th IEEE International Conference on BioInformatics and BioEngineering, Taichung, Taiwan
• [学会発表] A Network based Approach to Predict Functions of Metabolites (2018)
  • 著者名/発表者名: Md. Altaf-Ul-Amin
  • 学会等名: International Conference on Metabolomics,
  • 国際学会
• [学会発表] Multifaceted analysis of sequence similarity based network of allergens (2018)
  • 著者名/発表者名: Yasue Aoyama
  • 学会等名: International Conference on Computational Mathematics , Physics and It's Applications
  • 国際学会
• [図書] Applications of Network Clustering in Natural Product Research, In book: Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2020)
  • 著者名/発表者名: Altaf-Ul-Amin, M., & Kanaya, S.
  • 総ページ数: 33
  • 出版者: Elsevier
• [図書] Databases for Natural Product Research, In book: Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2020)
  • 著者名/発表者名: Kanaya, S., Altaf-Ul-Amin, M., Aki, M. H., Huang, M., & Ono, N.
  • 総ページ数: 16
  • 出版者: Elsevier
• [図書] Volatile Organic Compound Analysis in Biomedical Diagnosis Applications(Chapter 9) (2018)
  • 著者名/発表者名: Azian Azamimi Abdullah, Md. Altaf-Ul-Amin, and Shigehiko Kanaya
  • 総ページ数: 20
  • 出版者: Apple Academic Press
  • ISBN: 9781771887441
• [図書] Investigating Metabolic Pathways and Networks, In the book: Reference Module in Life Sciences (2018)
  • 著者名/発表者名: Altaf-Ul-Amin, M., Mohamed-Hussein, Z.-A., & Kanaya, S
  • 総ページ数: 16
  • 出版者: Elsevier
• [備考] DPClusO & BiClusO (DPClusSBO1.1)
  • URL: http://www.knapsackfamily.com/GRAPH_CLUSTERING/