Breast Cancer Candidate Gene Detection Through Integration of Subcellular Localization Data With Protein–Protein Interaction Networks

Abstract

Due to technological advances the quality and availability of biological data has increased dramatically in the last decade. Analysing protein-protein interaction networks (PPINs) in an integrated way, together with subcellular compartment data, provides such biological context, helps to fill in the gaps between a single type of biological data and genes causing diseases and can identify novel genes related to disease. In this study, we present BCCGD, a method for integrating subcellular localization data with PPINs that detects breast cancer candidate genes in protein complexes. We achieve this by defining the significance of the compartment, constructing edge-weighted PPINs, finding protein complexes with a non-negative matrix factorization approach, generating disease-specific networks based on the known disease genes, prioritizing disease candidate genes with a WDC method. As a case study, we investigate the breast cancer but the techniques described here are applicable to other disorders. For the top genes scored by BCCGD approach, we utilize the literature retrieving method to test the correlations of them with the breast cancer. The results show that BCCGD discover some novel breast cancer candidate genes which are valuable references for the biomedical scientists.