Fig 1.
Differentially expressed genes in a gene expression microarray of 26 pairs of gastric cancer and noncancerous tissues.
A) Volcano plot showing the differential genes (red dots) in the expression microarray (P-value <0.01, FDR <0.01). B) Clustering heatmap showing the differential lncRNAs. Each column represents one sample and each row represents one differential lncRNA. C) Clustering heatmap showing the differential mRNAs. Each column represents one sample and each row represents one differential mRNA.
Table 1.
top 40 differential expressed mRNAs in gastric cancer
Table 2.
top 60 differential expressed lncRNAs in gastric cancer
Fig 2.
GO categories based on differential genes in the expression microarray.
A) The significant GO categories for up-regulated genes. B) The significant GO categories for down-regulated genes. P-value <0.01 and FDR <0.01 were used as a threshold to enroll significant GO categories.
Fig 3.
Interaction of GO categories (GO Tree) based on analyses of differential GO categories.
Red dots represent up-regulated GO categories and green dots represent down-regulated GO categories.
Fig 4.
Pathway analysis of differentially expressed genes according to the KEGG database.
A) Top-ranking up-regulated pathways identified by KEGG. B) Top-ranking down-regulated pathways identified by KEGG. Differential pathways are listed according to P-value <0.01 and FDR <0.01.C) Pathway-Act network showing the interaction of differential pathways. The red dots represent up-regulated pathways and the green dots represent down-regulated pathways.
Fig 5.
Gene-Act network of differential genes according to pathways in the database.
Red dots represent up-regulated genes and green dots represent down-regulated genes. The arrows indicate the connection and regulatory relationship between two genes. Genes that have more connections with other genes have a higher degree score.
Fig 6.
Co-expression network of genes differentially expressed between normal and cancer tissues.
A) Co-expressed genes and their network in noncancerous tissue. B) Co-expressed genes and their network in gastric cancer. The greater the value of K-score, the stronger the differentially expressed genes are co-expressed. The scale of the K-score is from 1 to 21 in normal tissue but from 1 to 5 in cancer tissue.
Table 3.
top 20 differential genes with highest Degree and K-Core in co-expression network