Protocol for Discovering Convergent Molecular Networks across Multi-Omics Datasets Using Network Propagation

Phenotypic outcomes arise from coordinated changes across molecular layers. Although multi-omics data capture complementary molecular signals, integrating them into coherent biological mechanisms remains challenging due to limited overlap at the gene level. Network propagation maps significant gene hits from each dataset onto a prior knowledge molecular interaction network and diffuses their signals to neighboring genes. Mathematical integration of propagated networks, followed by clustering and pathway enrichment, reveals shared molecular networks, pinpointing the core biology captured across orthogonal molecular layers.