Integrated bioinformatics analysis reveals key candidate genes and pathways in breast cancer

Abstract

Breast cancer (BC) is the leading malignancy in women worldwide, yet relatively little is known about the genes and signaling pathways involved in BC tumorigenesis and progression. The present study aimed to elucidate potential key candidate genes and pathways in BC. Five gene expression profile data sets (GSE22035, GSE3744, GSE5764, GSE21422 and GSE26910) were downloaded from the Gene Expression Omnibus (GEO) database, which included data from 113 tumorous and 38 adjacent non-tumorous tissue samples. Differentially expressed genes (DEGs) were identified using t-tests in the limma R package. These DEGs were subsequently investigated by pathway enrichment analysis and a protein-protein interaction (PPI) network was constructed. The most significant module from the PPI network was selected for pathway enrichment analysis. In total, 227 DEGs were identified, of which 82 were upregulated and 145 were downregulated. Pathway enrichment analysis results revealed that the upregulated DEGs were mainly enriched in ‘cell division’, the ‘proteinaceous extracellular matrix (ECM)’, ‘ECM structural constituents’ and ‘ECM-receptor interaction’, whereas downregulated genes were mainly enriched in ‘response to drugs’, ‘extracellular space’, ‘transcriptional activator activity’ and the ‘peroxisome proliferator-activated receptor signaling pathway’. The PPI network contained 174 nodes and 1,257 edges. DNA topoisomerase 2-a, baculoviral inhibitor of apoptosis repeat-containing protein 5, cyclin-dependent kinase 1, G2/mitotic-specific cyclin-B1 and kinetochore protein NDC80 homolog were identified as the top 5 hub genes. Furthermore, the genes in the most significant module were predominantly involved in ‘mitotic nuclear division’, ‘mid-body’, ‘protein binding’ and ‘cell cycle’. In conclusion, the DEGs, relative pathways and hub genes identified in the present study may aid in understanding of the molecular mechanisms underlying BC progression and provide potential molecular targets and biomarkers for BC.

Prospective molecular mechanism of COL5A1 in breast cancer based on a microarray, RNA sequencing and immunohistochemistry

“…The immunohistochemical results were verified via the Human Protein Atlas (HPA; ) (29,30). The website aims at mapping the distribution of human proteins in cells, tissues and organs using integration technologies.…”

Integrated Bioinformatics Analysis the Function of RNA Binding Proteins (RBPs) and Their Prognostic Value in Breast Cancer

“…Currently, genes and signaling pathways that participate in breast cancer tumorigenesis and progression remain to be further investigated. Exploring new genes and pathways associated with breast cancer may help to identify potential molecular mechanisms, diagnostic markers and therapeutic targets (Wang et al, 2018). High-throughput genomic analysis techniques can be applied to screening for differentially expressed genes (DEGs) and to understand the relevant pathways and protein interaction networks (Vogelstein et al, 2013).…”

Comprehensive network analysis of integrin α11 expressed in human breast cancer

“…The combined application of these valuable microarray data allows us to build high-resolution networks (Fig 2) that contain useful information to detect gene regulatory networks in biological processes [7]. This suggests that we can perform co-expression screening using reliable network datasets and an effective human cancer database to track the genes involved in specific biological events [11]. In this study, 62 genes with high correlation with ITGA11 were identified as hub genes based on the UniProtKB keyword enrichment analysis.…”