Cited by 258Bioinformatics and Genomic NetworksMicrobial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

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

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Yugi, Katsuyuki, Kubota, Hiroyuki, Hatano, Atsushi, Kuroda, Shinya·2016·Trends in Biotechnology

DOI 10.1016/j.tibtech.2015.12.013

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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.

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Authors: Yugi, K., Kubota, H., Hatano, A., & Kuroda, S.
Affiliations: Japan Science and Technology Agency (JP)
Kyushu University (JP)
The University of Tokyo (JP)
Corresponding author: Yugi, Katsuyuki
Kuroda, Shinya
ORCID: Yugi, Katsuyuki
Kubota, Hiroyuki
Hatano, Atsushi
Kuroda, Shinya
Venue: Trends in Biotechnology
Publisher: Elsevier BV
Published: 2016-04
Volume: 34
Issue: 4
Pages: 276-290
ISSN: 0167-7799 (ISSN-L)
DOI: 10.1016/j.tibtech.2015.12.013
OpenAlex: W2274879598
Cited by: 258
References: 140
Citations by year: 2026: 7 · 2025: 13 · 2024: 19 · 2023: 18 · 2022: 29 · 2021: 23 · 2020: 43 · 2019: 38 · 2018: 32 · 2017: 25 · 2016: 11
FWCI: 3.19
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (am, 356 d)
doi.org/10.15223/policy-017 (stm-asf)
doi.org/10.15223/policy-037 (stm-asf)
doi.org/10.15223/policy-012 (stm-asf)
doi.org/10.15223/policy-029 (stm-asf)
doi.org/10.15223/policy-004 (stm-asf)
Locations: Trends in biotechnology (acceptedVersion)
PubMed (publishedVersion)
Funders: Japan Society for the Promotion of Science (15H05582)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords: trans-omics, multi-omics integration, metabolic networks, biochemical interactions, lifestyle-related diseases, genetic and environmental factors
MeSH terms: Computational Biology, Gene Regulatory Networks, Metabolic Networks and Pathways, Protein Interaction Maps

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

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