  Proteins interact with other proteins within biological pathways, forming
connected subgraphs in the protein-protein interactome (PPI). Proteins are
often involved in multiple biological pathways which complicates interpretation
of interactions between proteins. Gene expression data can assist our inference
since genes within a particular pathway tend to have more correlated expression
patterns than genes from distinct pathways. We provide an algorithm that uses
gene expression information to remove inter-pathway protein-protein
interactions, thereby simplifying the structure of the protein-protein
interactome. This refined topology permits easier interpretation and greater
biological coherence of multiple biological pathways simultaneously.

Molecular Networks