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.
@article{arxiv.1003.2811,
title = {Refining the Protein-Protein Interactome using Gene Expression Data},
author = {Sira Sriswasdi and Shane T. Jensen},
journal= {arXiv preprint arXiv:1003.2811},
year = {2012}
}