Weighted gene co-expression network analysis reveals modules and hub genes associated with the development of breast cancer

This study aimed to identify modules associated with breast cancer (BC) development by constructing a gene co-expression network, and mining hub genes that may serve as markers of invasive breast cancer (IBC).We downloaded 2 gene expression datasets from the Gene Expression Omnibus (GEO) database, a...

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Bibliographic Details
Published in:Medicine (Baltimore) 2019-02, Vol.98 (6), p.e14345-e14345
Main Authors: Qiu, Juanjuan, Du, Zhenggui, Wang, Yao, Zhou, Yuting, Zhang, Yuanxin, Xie, Yanyan, Lv, Qing
Format: Article
Language:English
Subjects:
alpha Karyopherins - genetics
Biomarkers, Tumor
Breast Neoplasms - genetics
Carcinoma, Ductal - genetics
Cell Adhesion
Cell Cycle
Cell Movement
Epithelial Cell Adhesion Molecule - genetics
Exosomes
Gene Expression Profiling
Gene Regulatory Networks - genetics
Humans
Keratins - genetics
Observational Study
Oligonucleotide Array Sequence Analysis
Protein-Serine-Threonine Kinases - genetics
Proto-Oncogene Proteins - genetics
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Summary:This study aimed to identify modules associated with breast cancer (BC) development by constructing a gene co-expression network, and mining hub genes that may serve as markers of invasive breast cancer (IBC).We downloaded 2 gene expression datasets from the Gene Expression Omnibus (GEO) database, and used weighted gene co-expression network analysis (WGCNA) to dynamically study the changes of co-expression genes in normal breast tissues, ductal carcinoma in situ (DCIS) tissues, and IBC tissues. Modules that highly correlated with BC development were carried out functional enrichment analysis for annotation, visualization, and integration discovery. The hub genes detected by WGCNA were also confirmed using the Oncomine dataset.We detected 17 transcriptional modules in total and 4 - namely tan, greenyellow, turquoise, and brown - were highly correlated with BC development. The functions of these 4 modules mainly concerned cell migration (tan module, P = 3.03 × 10), the cell cycle (greenyellow module, P = 3.08 × 10), cell-cell adhesion (turquoise module, P = .002), and the extracellular exosome (brown module, P = 1.38 × 10). WGCNA also mined the hub genes, which were highly correlated with the genes in the same module and with BC development. The Oncomine database confirmed that the expressions levels of 6 hub genes were significantly higher in BC tissues than in normal tissues, with fold changes larger than 2 (all P 
ISSN:0025-7974
1536-5964
DOI:10.1097/MD.0000000000014345