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

2019 Fiscal Year Annual Research Report

• Project/Area Number: 17K00406
• Research Institution: Nara Institute of Science and Technology
• Principal Investigator: 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)
• Project Period (FY): 2017-04-01 – 2020-03-31
• Keywords: Metabolomics / Metabolic Network / Metabolite Activity / Systems Biology / Network Clustering / Algorithms

Outline of Annual Research Achievements

We collected metabolite activity data and structural information of metabolites from KNApSAcK database and constructed the structural similarity based network of metabolites. Also we developed a network clustering tool called DPClusSBO which we applied for function prediction of metabolites. Structural similarity between metabolites implies functional similarity between them. In light of this fact we propose a method for function prediction of secondary metabolites and published a paper. Also, we have done several other works utilizing the tool DPClusSBO. Based on the research related to this project, we got several publications during last year in good journals including IEEE TRANSACTIONS ON Computational Biology and Bioinformatics, BMC medical genomics, Applied Network Science etc.

Research Products

• [Journal Article] Discovery of inflammatory bowel disease-associated miRNAs using a novel bipartite clustering approach (2020)
  • Author(s): Altaf-Ul-Amin, M., Karim, M. B., Hu, P., Naoaki, O. N. O., & Kanaya, S.
  • Journal Title: BMC Medical Genomics Volume: 13(3) Pages: 1-10
  • DOI: https://doi.org/10.1186/s12920-020-0660-y
• [Journal Article] Graph cluster approach in identifying novel proteins and significant pathways involved in polycystic ovary syndrome (2020)
  • Author(s): Afiqah-Aleng, N., Altaf-Ul-Amin, M., Kanaya, S., & Mohamed-Hussein, Z. A.
  • Journal Title: Reproductive biomedicine online Volume: 40(2) Pages: 319-330
  • DOI: https://doi.org/10.1016/j.rbmo.2019.11.012
• [Journal Article] BiClusO: A novel biclustering approach and its application to species-VOC relationship data (2019)
  • Author(s): Mohammad Bozlul Karim, Ming Huang, Naoaki ONO, Shigehiko Kanaya, Md. Altaf-Ul Amin
  • Journal Title: IEEE/ACM transactions on computational biology and bioinformatics Volume: 2019 Pages: 1-12
  • DOI: DOI 10.1109/TCBB.2019.2914901
• [Journal Article] Implementation of BiClusO and its comparison with other biclustering algorithms (2019)
  • Author(s): Mohammad Bozlul Karim, Shigehiko Kanaya, Md. Altaf-Ul-Amin
  • Journal Title: Applied Network Science Volume: 4(1) Pages: 1-15
  • DOI: s41109-019-0180-x
• [Journal Article] Prediction of Metabolite Activities by Repetitive Clustering of the Structural Similarity Based Networks (2019)
  • Author(s): Wakamatsu, N., Huang, M., Ono, N., Altaf-Ul-Amin, M., & Kanaya, S.
  • Journal Title: Journal of Computer Aided Chemistry Volume: 20 Pages: 76-83
  • DOI: https://doi.org/10.2751/jcac.20.76
• [Presentation] Applications of KNApSAcK Database and DPClus Algorithm: Plants to Metabolites to Target Proteins in the Context of Jamu Medicines and IBD Gene Prediction (2020)
  • Author(s): Md. Altaf-Ul-Amin
  • Organizer: Asian Regional Conference on Systems Biology
  • Int'l Joint Research
• [Presentation] 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)
  • Author(s): Md. Altaf-Ul-Amin
  • Organizer: University of south Australia, Adelaide
  • Invited
• [Presentation] Inter Disease Relations Based on Human Biomarkers by Network Analysis (2019)
  • Author(s): Md. Altaf-Ul-Amin
  • Organizer: IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)
  • Int'l Joint Research
• [Presentation] Discovery of inflammatory bowel disease-associated miRNAs using a novel bipartite clustering approach (2019)
  • Author(s): Md. Altaf-Ul-Amin
  • Organizer: International Conference on Genome Informatics (GIW 2019)
  • Int'l Joint Research
• [Presentation] Development of an Integrated System for Clustering of Simple and Bipartite Graphs and its Application to Different Types of Biological Data (2019)
  • Author(s): Md. Altaf-Ul-Amin
  • Organizer: University of Manitoba, Canada
  • Invited
• [Book] Applications of Network Clustering in Natural Product Research, In book: Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2020)
  • Author(s): Altaf-Ul-Amin, M., & Kanaya, S.
  • Total Pages: 33
  • Publisher: Elsevier
  • ISBN: ISBN: 978-0-12-409547-2
• [Book] Databases for Natural Product Research, In book: Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2020)
  • Author(s): Kanaya, S., Altaf-Ul-Amin, M., Aki, M. H., Huang, M., & Ono, N.
  • Total Pages: 16
  • Publisher: Elsevier
  • ISBN: ISBN: 978-0-12-409547-2
• [Remarks] DPClusO & BiClusO (DPClusSBO1.1)
  • URL: http://www.knapsackfamily.com/GRAPH_CLUSTERING/