Table 1.
Characteristics of the microarray datasets.
Fig 1.
DEGs in GSE104749, GSE3325, GSE69223, GSE46602.
(A-D) Volcano plots of all genes in four GEO databases. Red plots represented upregulated genes, green represented downregulated genes, the black plots represented the genes with no significant changes in expression. (A) GSE3325. (B) GSE46602. (C) GSE69223. (D) GSE104749. (E) Venn diagram of DEGs in four databases. The green, yellow, red, purple colors represented the DEGs of GSE46602, GSE69223, GSE104749, GSE3325, respectively. The number on the crossing area indicated the cross DEGs that were owned by different databases. (F) Upregulated genes co-expressed in the four databases. (G) Downregulated genes co-expressed in the four databases.
Fig 2.
(A-D) The bubble plots indicated the results of function enrichment analysis in DEGs. (A) Biological process. (B) Cell component. (C) Molecular function. (D) KEGG pathways. (E-F) Different expression genes enriched in the specific tissues and cell lines.
Fig 3.
Construction of PPI network and identification of candidate hub genes.
(A) PPI network. Red nodes represented upregulated genes while green represented downregulated genes. (B-D) Three different methods of cytoHubba were preformed to identify the hub genes. The top ten nodes are shown with a color scheme from red (highly important) to green (important). (B) Top ten genes in the PPI network were calculated by MCC. (C) Top ten genes in the PPI network were selected by Degree as candidates. (D) Top ten genes in the PPI network were selected by DNMC.
Fig 4.
Validation the expression and disease-free survival (DFS) of candidate hub genes in TCGA.
(A) UBE2C. (B) CCNB1. (C) TOP2A. (D) MKI67. (E) CDKN3. (F) PBK. (G) AURKA.
Fig 5.
The correlations between candidate hub genes and Gleason score.
UBE2C. (B) CCNB1. (C) TOP2A. (D) MKI67. (E) CDKN3. (F) PBK. (G) AURKA. *: p<0.05; **: p<0.01; ***: p<0.001; ****: p<0.0001.
Fig 6.
The correlations between UBE2C and clinical parameters.
(A) The expression level of UBE2C of benign prostate tissue, prostate cancer and castration-resistant prostate cancer in GSE70770 (left), TCGA (middle) and GSE116918 (right). (B) The relationship between Gleason score and UBE2C in TCGA. (C) The relationship between T-stage and UBE2C in TCGA. (D) The relationship between N-stage and UBE2C in TCGA. *: p<0.05; **: p<0.01; ***: p<0.001; ****: p<0.0001.
Fig 7.
Survival analysis and ROC curve of UBE2C in GSE70770 and TCGA.
(A) Disease free survival of patients based on the expression of UBE2C in GSE70770. (B) Disease free survival of patients based on the expression of UBE2C in TCGA. (C) ROC curve of UBE2C in GSE70770. (D) ROC curve of UBE2C in TCGA. (E-F) Time-dependent ROC curves. The AUCs at 1, 3, and 5 years were used to assess prognostic accuracy (left: GSE70770, right: TCGA). *: p<0.05; **: p<0.01; ***: p<0.001; ****: p<0.0001.
Table 2.
The relationships between UBE2C and clinical parameters (n = 203).
Table 3.
Univariate and multivariate Cox regression analysis for prostate cancer relapse-free survival.
Fig 8.
The results above all meet the standards (FDR<0.25, P-value < 0.05). The results showed that high expression of UBE2C were enriched in G2M check point, cell cycle, DNA replication, E2F targets, MYC targets, Notch signaling pathway.