Proteins interact with other proteins within biological pathways, forming connected subgraphs in the protein-protein interactome (PPI). However, proteins are often involved in multiple biological pathways which complicates inference about interactions between proteins. Gene expression data is informative here 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  of multiple biological pathways simultaneously.
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.
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However, proteins
Proteins
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inference about
interpretation of
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is informative here
can assist our inference
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and greater biological coherence