Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics

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.