Refining the Protein-Protein Interactome using Gene Expression Data

TL;DR

This paper introduces an algorithm that leverages gene expression data to refine the protein-protein interactome, removing inter-pathway interactions to improve interpretability and biological coherence.

Contribution

The novel algorithm uses gene expression correlations to systematically eliminate inter-pathway interactions in the PPI network.

Findings

Enhanced interpretability of PPI networks.

Improved biological coherence of pathways.

Facilitated analysis of complex biological interactions.

Abstract

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.