Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers

Katsuyuki Yugi; Hiroyuki Kubota; Atsushi Hatano; Shinya Kuroda

doi:10.1016/j.tibtech.2015.12.013

Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers

Trends Biotechnol. 2016 Apr;34(4):276-290. doi: 10.1016/j.tibtech.2015.12.013. Epub 2016 Jan 21.

Authors

Katsuyuki Yugi¹, Hiroyuki Kubota², Atsushi Hatano³, Shinya Kuroda⁴

Affiliations

¹ Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; PRESTO, Japan Science and Technology Agency, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: yugi@bs.s.u-tokyo.ac.jp.
² Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan; PRESTO, Japan Science and Technology Agency, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.
³ Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.
⁴ Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; CREST, Japan Science and Technology Agency, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: skuroda@bs.s.u-tokyo.ac.jp.

PMID: 26806111
DOI: 10.1016/j.tibtech.2015.12.013

Abstract

We propose 'trans-omic' analysis for reconstructing global biochemical networks across multiple omic layers by use of both multi-omic measurements and computational data integration. We introduce technologies for connecting multi-omic data based on prior knowledge of biochemical interactions and characterize a biochemical trans-omic network by concepts of a static and dynamic nature. We introduce case studies of metabolism-centric trans-omic studies to show how to reconstruct a biochemical trans-omic network by connecting multi-omic data and how to analyze it in terms of the static and dynamic nature. We propose a trans-ome-wide association study (trans-OWAS) connecting phenotypes with trans-omic networks that reflect both genetic and environmental factors, which can characterize several complex lifestyle diseases as breakdowns in the trans-omic system.

Keywords: metabolome; omic data; proteome; trans-ome-wide association study (trans-OWAS); trans-omics.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Computational Biology / methods*
Gene Regulatory Networks
Metabolic Networks and Pathways*
Protein Interaction Maps