Table 1.
Primers used for qPCR.
Fig 1.
Significant pathways of 980 differentially expressed genes.
A, Gene ontology analysis; B, KEGG analysis.
Fig 2.
Bi-clusters analysis of 45 differentially expressed miRNAs in gastric cancer vs. normal tissues.
Each row represents a miRNA and each column represents a sample. The “C” columns at the bottom represent cancer tissues, while “N” represents normal tissues. Red stands for high expression in cancer compared to normal tissue, while green for low expression in cancer compared to normal tissues.
Fig 3.
Bi-clusters analysis of 105 differentially expressed genes in TF-gene regulatory network.
Each row represents a miRNA and each column represents a sample. The “C” columns at the bottom represent cancer tissues, while “N” represents normal tissues. Red stands for high expression in cancer compared to normal tissue, while green for low expression in cancer compared to normal tissues.
Fig 4.
Significant pathways of 105 differentially expressed genes regulated by TF-gene regulatory network.
A, Gene ontology analysis; B, KEGG analysis.
Fig 5.
The E2F-related TF-miRNA network in gastric cancer tissues.
This network contains 105 differentially expressed genes and 9 differentially expressed miRNAs. Blue circles are differentially expressed genes and the red diamonds are differentially expressed miRNAs. The yellow rhombuses are TFs and its size represents the numbers of target genes. The direction of the arrow is from the source to the target.
Fig 6.
Validation of differential expression of mRNAs using qRT-PCR.
Gene expression was analyzed in 10 paired gastric cancerous and normal tissues and compared to microarray results. The columns in the chart represent the log-transformed median fold changes (cancer/control) in expression across ten samples (p<0.05).
Fig 7.
Detection of the hub genes based on The E2F-related TF-miRNA network analysis.
Circles are hub genes that co-regulated by TFs and miRNAs, while the red diamonds are differentially expressed miRNAs. The yellow rhombuses are TFs and its size represents the numbers of target genes. The direction of the arrow is from the source to the target.
Table 2.
Significant GO pathways of the hub-genes regulated by the TF-miRNA co-regulatory network.
Fig 8.
ROC curve as discriminators between cancer and normal tissues.
AUC, Area under the ROC Curve; All indicates the combination of E2F1, E2F2, E2F3, E2F4, E2F5, and E2F7.
Fig 9.
Expression of E2F1, E2F2, E2F3, E2F4, E2F5, and E2F7 mRNAs associated with the depth of gastric cancer invasion.
Microarray data from 45 gastric cancer cases were used to analyze association between E2F family and gastric cancer invasion. Gastric cancer invasion was referred to the International Union against Cancer (UICC) TNM staging system. T1, Tumor invades lamina propria, muscularis mucosae, or submucosa; T2, Tumor invades muscularispropria; T3, Tumor penetrates subserosal connective tissue without invasion of visceral peritoneum or adjacent structures; T4, Tumor invades serosa (visceral peritoneum) or adjacent structures.
Fig 10.
Expression of E2F1, E2F2, E2F3, E2F4, E2F5, and E2F7 mRNAs associated with gastric cancer differentiation.