TCGA analysis of SOX9. (A) Pathway analysis from MetaCore for SOX9 reveals many pathways involved in EMT. (B) Median survival time for patients with high SOX9 expression is 3.9 years (n = 74). Median survival time for patients with low SOX9 expression is 5.8 years (n = 74). The difference in survival is significant (P <0.05). (C) Survival analysis for high and low SOX9 expression segregated into primary, lymph node, and metastatic cohorts. (D) Pie charts displaying the number of SOX9 target genes that have a contribution to patient survival. (E) ChIP analysis for SOX9 binding targets. Enrichment of the promoter regions for TMEM158, TBX3, and FYB were similar to positive controls COL2A1, p21, and SOX10 and greater than negative control IP10. Data are shown as bound vs. input. Error bars indicate standard error of the mean of three independent experiments. IgG controls not shown on graph because they were below detection limit.