title: Data Mining Methods for Omics and Knowledge of Crude Medicinal Plants toward Big Data Biology.
abstract: Molecular biological data has rapidly increased with the recent progress of the Omics fields, e.g., genomics, transcriptomics, proteomics and metabolomics that necessitates the development of databases and methods for efficient storage, retrieval, integration and analysis of massive data. The present study reviews the usage of KNApSAcK Family DB in metabolomics and related area, discusses several statistical methods for handling multivariate data and shows their application on Indonesian blended herbal medicines (Jamu) as a case study. Exploration using Biplot reveals many plants are rarely utilized while some plants are highly utilized toward specific efficacy. Furthermore, the ingredients of Jamu formulas are modeled using Partial Least Squares Discriminant Analysis (PLS-DA) in order to predict their efficacy. The plants used in each Jamu medicine served as the predictors, whereas the efficacy of each Jamu provided the responses. This model produces 71.6% correct classification in predicting efficacy. Permutation test then is used to determine plants that serve as main ingredients in Jamu formula by evaluating the significance of the PLS-DA coefficients. Next, in order to explain the role of plants that serve as main ingredients in Jamu medicines, information of pharmacological activity of the plants is added to the predictor block. Then N-PLS-DA model, multiway version of PLS-DA, is utilized to handle the three-dimensional array of the predictor block. The resulting N-PLS-DA model reveals that the effects of some pharmacological activities are specific for certain efficacy and the other activities are diverse toward many efficacies. Mathematical modeling introduced in the present study can be utilized in global analysis of big data targeting to reveal the underlying biology.
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan ; Department of Statistics, Bogor Agricultural University, Jln. Meranti, Kampus IPB Darmaga, Bogor 16680, Indonesia.
authors.forename: Farit M
authors.initials: FM
authors.lastname: Afendi
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan.
authors.forename: Naoaki
authors.initials: N
authors.lastname: Ono
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan.
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Nakamura
authors.affiliation: Maebashi Institute of technology, 450-1 Kamisadori, Maebashi-shi, Gunma, 371-0816 Japan.
authors.forename: Kensuke
authors.initials: K
authors.lastname: Nakamura
authors.affiliation: Biopharmaca Research Center, Bogor Agricultural University, Kampas IPB Taman Kencana, Jln. Taman Kencana No. 3 Bogor 16151, Indonesia.
authors.forename: Latifah K
authors.initials: LK
authors.lastname: Darusman
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan.
authors.forename: Nelson
authors.initials: N
authors.lastname: Kibinge
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan.
authors.forename: Aki Hirai
authors.initials: AH
authors.lastname: Morita
authors.affiliation: Department of Medicinal Resources, Institute of Natural Medicine, University of Toyama, 2630 Toyama, 930-0194, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Tanaka
authors.affiliation: Department of Electronic and Computer Engineering, Ibaraki National College of Technology, 866 Nakane, Hitachinaka, Ibaraki 312-8508, Japan.
authors.forename: Hisayuki
authors.initials: H
authors.lastname: Horai
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan.
authors.forename: Md
authors.initials: M
authors.lastname: Altaf-Ul-Amin
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, Nara 630-0101, Ikoma, Japan.
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya