Dataset Information

Identification of crucial genes in abdominal aortic aneurysm by WGCNA.

ABSTRACT: Background:Abdominal aortic aneurysm (AAA) is the full thickness dilation of the abdominal aorta. However, few effective medical therapies are available. Thus, elucidating the molecular mechanism of AAA pathogenesis and exploring the potential molecular target of medical therapies for AAA is of vital importance. Methods:Three expression datasets (GSE7084, GSE47472 and GSE57691) were downloaded from the Gene Expression Omnibus (GEO). These datasets were merged and then normalized using the "sva" R package. Differential expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were conducted. We compared the co-expression patterns between AAA and normal conditions, and hub genes of each functional module were identified. DEGs were mapped to co-expression network under AAA condition and a DEG co-expression network was generated. Crucial genes were identified using molecular complex detection (MCODE) (a plugin in Cytoscape). Results:In our study, 6 and 10 gene modules were detected for the AAA and normal conditions, respectively, while 143 DEGs were screened. Compared to the normal condition, genes associated with immune response, inflammation and muscle contraction were clustered in three gene modules respectively under the AAA condition; the hub genes of the three modules were MAP4K1, NFIB and HPK1, respectively. A DEG co-expression network with 102 nodes and 303 edges was identified, and a hub gene cluster with 10 genes from the DEG co-expression network was detected. YIPF6, RABGAP1, ANKRD6, GPD1L, PGRMC2, HIGD1A, GMDS, MGP, SLC25A4 and FAM129A were in the cluster. The expression levels of these 10 genes showed potential diagnostic value. Conclusion:Based on WGCNA, we detected 6 modules under the AAA condition and 10 modules in the normal condition. Hub genes of each module and hub gene clusters of the DEG co-expression network were identified. These genes may act as potential targets for medical therapy and diagnostic biomarkers. Further studies are needed to elucidate the detailed biological function of these genes in the pathogenesis of AAA.

SUBMITTER: Chen S

PROVIDER: S-EPMC6788446 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Identification of crucial genes in abdominal aortic aneurysm by WGCNA.

Chen Siliang S Yang Dan D Lei Chuxiang C Li Yuan Y Sun Xiaoning X Chen Mengyin M Wu Xiao X Zheng Yuehong Y

PeerJ 20191008

<h4>Background</h4>Abdominal aortic aneurysm (AAA) is the full thickness dilation of the abdominal aorta. However, few effective medical therapies are available. Thus, elucidating the molecular mechanism of AAA pathogenesis and exploring the potential molecular target of medical therapies for AAA is of vital importance.<h4>Methods</h4>Three expression datasets (GSE7084, GSE47472 and GSE57691) were downloaded from the Gene Expression Omnibus (GEO). These datasets were merged and then normalized u ...[more]

PMID: 31608184

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Project description:BackgroundWith a mortality rate of 65-85%, a ruptured abdominal aortic aneurysm (AAA) can have catastrophic consequences for patients. However, few effective pharmaceutical treatments are available to treat this condition. Therefore, elucidating the pathogenesis of AAA and finding the potential molecular targets for medical therapies are vital lines of research.MethodsAn mRNA microarray dataset of perivascular adipose tissue (PVAT) in AAA patients was downloaded and differentially expressed gene (DEG) screening was performed. Weighted gene co-expression networks for dilated and non-dilated PVAT samples were constructed via weighted correlation network analysis (WGCNA) and used to detect gene modules. Functional annotation analysis was performed for the DEGs and gene modules. We identified the hub genes of the modules and created a DEG co-expression network. We then mined crucial genes based on this network using Molecular Complex Detection (MCODE) in Cytoscape. Crucial genes with top-6 degree in the crucial gene cluster were visualized, and their potential clinical significance was determined.ResultsOf the 173 DEGs screened, 99 were upregulated and 74 were downregulated. Co-expression networks were built and we detected 6 and 5 modules for dilated and non-dilated PVAT samples, respectively. The turquoise and black modules for dilated PVAT samples were related to inflammation and immune response. MAP4K1 and PROK2 were the hub genes of these 2 modules, respectively. Then a DEG co-expression network with 112 nodes and 953 edges was created. PLAU was the crucial gene with the highest connectivity and showed potential clinical significance.ConclusionsUsing WGCNA, gene modules were detected and hub genes and crucial genes were identified. These crucial genes might be potential targets for pharmaceutic therapies and have potential clinical significance. Future in vitro and in vivo experiments are required to more comprehensively explore the biological mechanisms by which these genes affect AAA pathogenesis.

Dataset Information

Identification of crucial genes in abdominal aortic aneurysm by WGCNA.

Publications

Identification of crucial genes in abdominal aortic aneurysm by WGCNA.

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