Peer Review #2 of "The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes (v0.1)" [peer_review]

2019 unpublished
In general, type 2 diabetes (T2D) usually occurs in middle-aged and elderly people. However, the incidence of childhood-onset T2D has increased all across the globe. Therefore, it is very important to determine the molecular and genetic mechanisms of childhood-onset T2D. In this study, the dataset GSE9006 was downloaded from the GEO (Gene Expression Omnibus database); it includes 24 healthy children, 43 children with newly diagnosed Type 1 diabetes (T1D), and 12 children with newly diagnosed
more » ... . These data were used for differentially expressed genes (DGEs) analysis and weighted coexpression network analysis (WGCNA). We identified 192 up-regulated genes and 329 down-regulated genes by performing DEGs analysis. By performing WGGNA, we found that blue module (539 genes) was highly correlated to cyan module (97 genes). Gene ontology (GO) and pathway enrichment analyses were performed to figure out the functions and related pathways of genes, which were identified in the results of DEGs and WGCNA. Genes with conspicuous logFC and in the high correlated modules were input into GeneMANIA, which is a plugin of Cytoscape application. Thus, we constructed the proteinprotein interaction (PPI) network (92 nodes and 254 pairs). Eventually, we analyzed the transcription factors and references related to genes with conspicuous logFC or highdegree genes, which were present in both the modules of WGCNA and PPI network. Current research shows that EGR1 and NAMPT can be used as marker genes for childhoodonset T2D. Gestational diabetes and chronic inflammation are risk factors that lead to the development of childhood-onset T2D. PeerJ reviewing PDF | (Abstract 13 In general, type 2 diabetes (T2D) usually occurs in middle-aged and elderly people. 14 However, the incidence of childhood-onset T2D has increased all across the globe. Therefore, it 15 is very important to determine the molecular and genetic mechanisms of childhood-onset T2D. 16 In this study, the dataset GSE9006 was downloaded from the GEO (Gene Expression Omnibus 17 database); it includes 24 healthy children, 43 children with newly diagnosed Type 1 diabetes 18 (T1D), and 12 children with newly diagnosed T2D. These data were used for differentially 19 expressed genes (DGEs) analysis and weighted co-expression network analysis (WGCNA). We 20 identified 192 up-regulated genes and 329 down-regulated genes by performing DEGs analysis. 21 By performing WGGNA, we found that blue module (539 genes) was highly correlated to cyan 22 module (97 genes). Gene ontology (GO) and pathway enrichment analyses were performed to 23 figure out the functions and related pathways of genes, which were identified in the results of 24 DEGs and WGCNA. Genes with conspicuous logFC and in the high correlated modules were 25 input into GeneMANIA, which is a plugin of Cytoscape application. Thus, we constructed the 26 protein-protein interaction (PPI) network (92 nodes and 254 pairs). Eventually, we analyzed the 27 transcription factors and references related to genes with conspicuous logFC or high-degree PeerJ reviewing PDF | (Manuscript to be reviewed 28 genes, which were present in both the modules of WGCNA and PPI network. Current research 29 shows that EGR1 and NAMPT can be used as marker genes for childhood-onset T2D. 30 Gestational diabetes and chronic inflammation are risk factors that lead to the development of 31 childhood-onset T2D. 32
doi:10.7287/peerj.6343v0.1/reviews/2 fatcat:62mhmf2mmbbmnkcxlyhjor5gji