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Peer Review #1 of "Identification of crucial genes in abdominal aortic aneurysm by WGCNA (v0.2)" [peer_review]

2019 unpublished
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
more » ... 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 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 3 gene modules respectively under the AAA condition; the hub genes of the 3 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. PeerJ reviewing PDF | Abstract 39 Background: Abdominal aortic aneurysm (AAA) is the full thickness dilation of the abdominal 40 aorta. However, few effective medical therapies are available. Thus, elucidating the molecular 41 mechanism of AAA pathogenesis and exploring the potential molecular target of medical therapies 42 for AAA is of vital importance. 43 Methods: Three expression datasets (GSE7084, GSE47472 and GSE57691) were downloaded 44 from the Gene Expression Omnibus (GEO). These datasets were merged and then normalized 45 using the "sva" R package. Differential expressed gene (DEG) analysis and weighted gene co-46 expression network analysis (WGCNA) were conducted. We compared the co-expression patterns 47 between AAA and normal conditions, and hub genes of each functional module were identified. 48 DEGs were mapped to co-expression network under AAA condition and a DEG co-expression 49 network was generated. Crucial genes were identified using MCODE (a plugin in Cytoscape). 50 Results: In our study, 6 and 10 gene modules were detected for the AAA and normal conditions, 51 respectively, while 143 DEGs were screened. Compared to the normal condition, genes associated 52 with immune response, inflammation and muscle contraction were clustered in 3 gene modules 53 respectively under the AAA condition; the hub genes of the 3 modules were MAP4K1, NFIB and 54 HPK1, respectively. A DEG co-expression network with 102 nodes and 303 edges was identified, 55 and a hub gene cluster with 10 genes from the DEG co-expression network was detected. YIPF6, 56 RABGAP1, ANKRD6, GPD1L, PGRMC2, HIGD1A, GMDS, MGP, SLC25A4 and FAM129A 57 were in the cluster. The expression levels of these 10 genes showed potential diagnostic value. 58 Conclusion: Based on WGCNA, we detected 6 modules under the AAA condition and 10 modules 59 in the normal condition. Hub genes of each module and hub gene clusters of the DEG co-60 expression network were identified. These genes may act as potential targets for medical therapy 61 and diagnostic biomarkers. Further studies are needed to elucidate the detailed biological function 62 of these genes in the pathogenesis of AAA.
doi:10.7287/peerj.7873v0.2/reviews/1 fatcat:2swkpzutvvbqfjzpnacbvll7oq