Basic Study
Copyright ©The Author(s) 2018.
World J Gastroenterol. Nov 21, 2018; 24(43): 4906-4919
Published online Nov 21, 2018. doi: 10.3748/wjg.v24.i43.4906
Figure 1
Figure 1 Volcano plot of the differentially expressed mRNAs between stomach adenocarcinoma and para-carcinoma tissues. Red indicates high expression and green indicates low expression (|log2FC| > 1 and adjusted P value < 0.05). The X axis represents a false discovery rate (FDR) value and the Y axis represents a log2FC. Differential mRNAs were calculated by edgeR. There were 2456 highly expressed and 3775 lowly expressed mRNAs. This volcano plot was conducted by the ggplot2 package of R language. FDR: False discovery rate.
Figure 2
Figure 2 Determination of soft-thresholding power in weighted gene co-expression network analysis and gene clustering dendrograms. A: Analysis of the scale-free fit index for various soft-thresholding powers (β); B: Analysis of the mean connectivity for various soft-thresholding powers; C: Gene clustering tree (dendrogram) obtained by hierarchical clustering of adjacency-based dissimilarity.
Figure 3
Figure 3 Identification of modules associated with clinical traits of stomach adenocarcinoma. A: Heat map of the correlation between module eigengenes and clinical traits of stomach adenocarcinoma (SA); B: Topological overlap matrix (TOM) plot; C: Visualization of hierarchical clustering dendrogram of the eigengenes. The eigen gene network represents the relationships among modules; D: Heat map of the eigengene adjacency. The color bars on the left and below indicate the module for each row or column.
Figure 4
Figure 4 Module functional annotation and hub gene identification. A and B: Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for genes in the tan-module. The X-axis shows the number of genes and the Y-axis shows the GO and KEGG terms; C: Weighted co-expression network for tan-module genes. (nodes are colored according to the degree, and sized according to the Molecular Complex Detection (MCODE) score); D: Hub genes were screened with module membership (MM), gene significance (GS) and MCODE. GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; GS: Gene significance; MM: Module membership; MCODE: Molecular Complex Detection.
Figure 5
Figure 5 Expression of sorting nexin 10 in stomach adenocarcinoma cells and tissue and its effect on survival. A: Sorting nexin 10 (SNX10) protein expression in stomach adenocarcinoma (SA) cell lines (SGC-7901 and BGC-823) and the human normal gastric epithelial cell line (GSE-1) by western blot. β-actin was used as a loading control; n = 3, aP < 0.05; B: SNX10 mRNA expression in SGC-7901, BGC-823 and GSE-1 by real time-PCR; n = 3, aP < 0.05; C: The representative negative result in SA tissue; magnifications are 200 ×; D: SNX10 was weakly expressed in SA tissue; magnifications are 200 ×; E: SNX10 had strong expression in SA tissue; magnifications are 200 ×; F: Disease free survival curves stratified by SNX10 expression (P = 0.00); G: Overall survival curves stratified by SNX10 expression (P = 0.00). DFS: Disease-free survival; OS: Overall survival; SNX10: Sorting nexin 10.