Identification of Hub Genes Using Co-Expression Network Analysis in Breast Cancer as a Tool to Predict Different Stages

Abstract

BackgroundBreast cancer has a high mortality rate and is the most common cancer of women worldwide. Our gene co-expression network analysis identified the genes closely related to the pathological stage of breast cancer.Material/MethodsWe performed weighted gene co-expression network analysis (WGCNA) from the Gene Expression Omnibus (GEO) database, and performed pathway enrichment analysis on genes from significant modules.ResultsA non-metastatic sample (374) of breast cancer from GSE102484 was used to construct the gene co-expression network. All 49 hub genes have been shown to be upregulated, and 19 of the 49 hub genes are significantly upregulated in breast cancer tissue. The roles of the genes CASC5, CKAP2L, FAM83D, KIF18B, KIF23, SKA1, GINS1, CDCA5, and MCM6 in breast cancer are unclear, so in order to better reveal the staging of breast cancer markers, it is necessary to study those hub genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes indicated that 49 hub genes were enriched to sister chromatid cohesion, spindle midzone, microtubule motor activity, cell cycle, and something else. Additionally, there is an independent data set – GSE20685 – for module preservation analysis, survival analysis, and gene validation.ConclusionsThis study identified 49 hub genes that were associated with pathologic stage of breast cancer, 19 of which were significantly upregulated in breast cancer. Risk stratification, therapeutic decision making, and prognosis predication might be improved by our study results. This study provides new insights into biomarkers of breast cancer, which might influence the future direction of breast cancer research.

GINS1/2/3/4 Upregulation Predicts Poor Prognosis in Human Sarcoma

“…Through the research by Bu et al, the levels of GINS1 also in connected with the development of pancreatic cancer [34]. This is also con rmed by the research of Fu et al [35]. Our study indicated that the value of GINS1 in prognosis of human sarcoma was con rmed by 131 sarcoma patients.…”

Identification of the hub genes RUNX2 and FN1 in gastric cancer

“…STRING database version 10.5 ( http://string-db.org ) was applied to evaluate the PPI information. DEGs were uploaded into STRING, a confidence score >0.9 defined them as significant [ 23 ], and then, the PPI network was constructed. We downloaded the resulting data in a table in a tab-separating values format.…”

“…The cytoHubba plug-in was used to identify the hub genes. A hub gene is defined as a gene with the highest degree of connectivity in the hub module [ 23 ]. The hub genes showed a strong association with other node proteins (more than 10) [ 23 ].…”

Recombination and Pol ζ Rescue Defective DNA Replication upon Impaired CMG Helicase—Pol ε Interaction

“…Mutations or deregulation of the human homolog of the PSF1 gene was observed in correlation with disorders involving cancer, neurodevelopmental, and immunodeficiency issues [ 71 , 72 , 73 , 74 , 75 , 76 , 77 ]. However, the precise role of GINS subunits in these processes is poorly understood.…”

“…The study of noncatalytic proteins of the CMGE complex is attracting greater attention, because mutations in genes encoding its subunits or changes in their expression have a significant impact on the development of cancer or genetic diseases [ 71 , 72 , 73 , 74 , 75 , 76 , 77 , 78 , 79 ]. In contrast to the role of DNA polymerases, which have been analyzed in detail, the influence of the noncatalytic components of the replisome on the DNA replication process remains poorly understood.…”