The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancer.

Copy number variations (CNVs) are one type of the human genetic variations and are pervasive in the human genome. It has been confirmed that they can play a causal role in complex diseases. Previous studies of CNVs focused more on identifying the disease-specific CNV regions or candidate genes on these CNV regions, but less on the synergistic actions between genes on CNV regions and other genes. Our research combined the CNVs with related gene co-expression to reconstruct gene co-expression network by using single nucleotide polymorphism microarray datasets and gene microarray datasets of breast cancer, and then extracted the modules which connected densely inside and analyzed the functions of modules. Interestingly, all of these modules' functions were related to breast cancer according to our enrichment analysis, and most of the genes in these modules have been reported to be involved in breast cancer. Our findings suggested that integrating CNVs and gene co-expressed relations was an available way to analyze the roles of CNV genes and their synergistic genes in breast cancer, and provided a novel insight into the pathological mechanism of breast cancer.