Multi-omic integration by machine learning (MIMaL)

Connections between molecules in different omic layers were discovered through a combination of machine learning and model interpretation. Discovered connections reflected protein control (ProC) over metabolites. Proteins discovered to control citrate were mapped onto known genetic and metabolic networks, revealing that these protein regulators are novel. Further, clustering the magnitudes of ProC over all metabolites enabled the prediction of five gene functions, each of which was validated experimentally. Two uncharacterized genes, YJR120W and YDL157C, were accurately predicted to modulate mitochondrial translation. Functions for three incompletely characterized genes were also predicted and validated, including SDH9, ISC1 and FMP52. A website enables results exploration and also MIMaL analysis of user-supplied multi-omic data. Availability and implementation: The website for MIMaL is at https://mimal.app. Code for the website is at https://github.com/qdickinson/mimal-website. Code to implement MIMaL is at https://github.com/jessegmeyerlab/MIMaL.

Supplementary data are available at Bioinformatics online.