Fig. 8

WGCNA and module-trait analysis of the downstream genes closely related to RP11-296E3.2, YBX1, and STAT3. A The best soft threshold (β) value was determined depending on scale-free topology and mean connectivity analysis of TCGA data of COAD patients. B Hierarchical clustering of the eigengene modules. C Correlations between the traits (RP11-296E3.2, YBX1, and STAT3 expression; patient age; tumor stage; and patient sex) and the eigengene modules were analyzed and are shown in the heatmap (R, version 3.5.1). D, E Top enriched pathways for the significantly correlated modules (MEblue and MEgray). F Venn diagram showing the overlapping genes in four comparison sets (MEblue and MEgray module genes and the SDEGs between the sh-Con and sh-RP11-296E3.2 groups). G mRNA levels of the 4 overlapping downregulated genes from the RNA-seq results. H The altered levels of the 4 overlapping downregulated genes were confirmed by qRT-PCR in HCT116 cells transduced with the indicated shRNAs. I Downregulation of RP11-296E3.2 expression weakened the effects of upregulated YBX1 mRNA expression. The data are presented as the means ± SDs. Statistical significance was assessed using one-way ANOVA followed by Tukey’s test for multiple comparisons. All experiments were performed with at least three biological duplicates (n = 3) for each group. *P < 0.05, **P < 0.01, ***P < 0.001