Fig. 7: Multi-omic network inference for the Parkinson’s disease datasets.

Time-series transcriptomic (upper) and metabolomic (lower) data for a PINK1 mutant and b healthy samples. Upper: Projection of the single-cell data using PCA. The arrow shows the pseudotime trajectory estimated by MINIE; the trajectory does not pass through the point clouds due to significant zero inflation in the data (which is accounted for by a weighting scheme described in “Methods” section). Lower: Bulk metabolic concentrations (dots) and inferred metabolomic trajectories (dashed lines) using MINIE's transcriptome–metabolome mapping. For illustration purposes, just two metabolites are shown: phenylalanine (purple) and glutamate (blue). c Histograms of predicted probability values for the existence of each link, considering gene-gene interactions (left panel), metabolite-to-gene interactions (middle panel), and perturbation targets (right panel). d Reconstructed network based on confidence values for ε₂ = 0.06. Only genes (purple) and metabolites (green) with regulatory links are included (node size is proportional to the degree of each node). PINK1, the gene responsible for the mutation under study, is highlighted in bold. e Reconstructed network for ε₁ = 0.04.