Identification of Diagnostic Markers for Breast Cancer Based on Differential Gene Expression and Pathway Network

TLDR: It is shown that the difference of gene expression level is important for the diagnosis of breast cancer, and 23 breast cancer diagnostic markers are identified, which provides valuable information for clinical diagnosis and basic treatment experiments.

Abstract: Background: Breast cancer is the second largest cancer in the world, the incidence of breast cancer continues to rise worldwide, and women’s health is seriously threatened. Therefore, it is very important to explore the characteristic changes of breast cancer from the gene level, including the screening of differentially expressed genes and the identification of diagnostic markers. Methods: The gene expression profiles of breast cancer were obtained from the TCGA database. The edgeR R software package was used to screen the differentially expressed genes between breast cancer patients and normal samples. The function and pathway enrichment analysis of these genes revealed significant enrichment of functions and pathways. Next, download these pathways from KEGG website, extract the gene interaction relations, construct the KEGG pathway gene interaction network. The potential diagnostic markers of breast cancer were obtained by combining the differentially expressed genes with the key genes in the network. Finally, these markers were used to construct the diagnostic prediction model of breast cancer, and the predictive ability of the model and the diagnostic ability of the markers were verified by internal and external data. Results: 1060 differentially expressed genes were identified between breast cancer patients and normal controls. Enrichment analysis revealed 28 significantly enriched pathways (p < 0.05). They were downloaded from KEGG website, and the gene interaction relations were extracted to construct the gene interaction network of KEGG pathway, which contained 1277 nodes and 7345 edges. The key nodes with a degree greater than 30 were extracted from the network, containing 154 genes. These 154 key genes shared 23 genes with differentially expressed genes, which serve as potential diagnostic markers for breast cancer. The 23 genes were used as features to construct the SVM classification model, and the model had good predictive ability in both the training dataset and the validation dataset (AUC = 0.960 and 0.907, respectively). Conclusion: This study showed that the difference of gene expression level is important for the diagnosis of breast cancer, and identified 23 breast cancer diagnostic markers, which provides valuable information for clinical diagnosis and basic treatment experiments.