Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics. Issue 15 (June 2019)

• Record Type: Journal Article
• Authors: Yugi, Katsuyuki; Ohno, Satoshi; Krycer, James R.; James, David E.; Kuroda, Shinya
• Is Part Of: Current opinion in systems biology. Issue 15(2019)
• Page Start: 109
• Page End: 120
• Publication Date: 2019-06
• Subjects: Systems biology -- Periodicals; 570
• DOI: 10.1016/j.coisb.2019.04.005
• Languages: English
• ISSNs: 2452-3100

Abstract

Abstract: We have presented 'trans-omics', a discipline that mechanistically connects multiple omic layers. The relationships between molecules of distinct omic layers are governed by reaction rate equations such as v = k [ S ] ( v : reaction rate; k : rate constant; [ S ]: concentration of molecule S ). However, because of the limited availability of the reaction rate data for the left-hand side of the equation, many studies use changes in the amount of molecules in the right-hand side as a surrogate for the reaction rate. Recent advances in comprehensive measurement technologies enable to measure reaction rates in several omic layers. This allows attributing trans-omic network reconstruction to model selection problem of differential equation-based models. Thus, rate-oriented trans-omics enables more mechanistic network reconstruction, instead of an empirical network reconstruction that uses concentrations as readouts of reaction rates. Graphical abstract: A trans-omic network reconstruction on the basis of reaction kinetics. Left: multi-omics integration studies often rely on correlation across omic layers in their attempts for data integration. Right: trans-omics studies implicitly or explicitly postulate differential equations behind multi-omic data to reconstruct mechanistic networks. Image 1 Highlights: Amounts of molecules cannot necessarily be readouts for reaction rates. Using rates instead of amounts allows more mechanistic network reconstruction. Novel measurement methods for reaction rates allow 'rate-oriented' trans-omics. Rate-oriented trans-omics provides mathematical models of multilayered networks.