Figure 4

Differentially expressed genes and enrichment analysis after knockdown of UBC9. (A) Heat map showed the expression of DEGs in each replicate. Samples (column) and genes (row) were clustered by unsupervised hierarchical cluster analysis. (B) Volcano plots showed the differential expression of genes between shRNA-UBC9 and shRNA-NC. Red dots represented the significantly upregulated genes in shRNA-UBC9 group compared with shRNA-NC group (Log2(foldchange) > 1 & FDR P < 0.05). Blue dots represented the significantly downregulated genes in shRNA-UBC9 group compared with shRNA-NC group (Log2(foldchange) < − 1 & FDR P < 0.05). Black dots represented non DEGs. (C) Scatterplot illustrated the expression of genes in the shRNA-UBC9 group and shRNA-NC group. The top 10 upregulated and top 10 downregulated genes with RPKM over 0.5 in shRNA-UBC9 group were marked. Reference line represented twofold change. (D) The expression of selected DEGs was validated by RT-qPCR. Data was generated from three independent studies. Means ± SD are shown. *P < 0.001. (E) The GOCircle plot showed the top 10 significant GO molecular function terms based on adjust P-value. The height of the bar in the inner ring suggested the significance of the corresponding term (− log10 adjusted P-value), and color corresponded to the z-score. The scatterplots plot in the out ring showed the expression level of genes (logFoldChange) in the corresponding term. The term IDs in the out ring corresponded to the description in the right table. (F) The map illustrated the results of GSEA. Red dots represented the pathways significantly upregulated in shRNA-UBC9 group. Blue dots represented the pathways significantly downregulated in shRNA-UBC9 group. Clusters of functionally related gene-sets were circled and assigned a representative label. (G) The top 4 most significant pathways identified by GSEA.