Schematic diagram representing two-layer network structure between genes and proteins. Nodes are coloured red in the gene layer. Each dotted hull shows an individual gene module of connected genes, based on their co-expression correlations. This is projected onto the protein layer to construct a primary network of expressed proteins, shown in blue. The secondary network of interacting proteins is highlighted in green. Each solid hull represents the protein module corresponding to the gene module. Protein submodules are shown within these modules. The accompanying flow-chart gives an overview of the protocol.