Research Paper Volume 11, Issue 22 pp 10316—10337

Figure 5. Copy number (CN) alterations of EDCGs affected their expression in advanced ccRCC. (A) The EDCGs located in the focal CN amplification peaks. False-discovery rates (q values) and scores generated by GISTIC 2.0 for amplifications (x-axis) are plotted against chromosome locations (y-axis). Dotted lines indicate the centromeres. The green line represents cut-off (q = 0.25) that determines statistical significance. (B) The expression of FOXM1 affected by expression quantitative trait CN (eQTCNs). (C) Clustering of CNAs of genes affected by eQTCNs. The deletion of genes with odds ratio (OR) <1 and FDR <0.05 was associated with advanced tumors. The amplification of genes with OR >1 and FDR <0.05 was related to advanced tumors. (D) Gene set enrichment analysis between ccRCC with regional/distant metastasis and localized tumors. (E) Overall survival and progression-free survival of ccRCC patients with FOXM1 amplifications versus those with FOXM1 wild type (WT). (F) The expression changes of FOXM1 between samples with FOXM1 amplification and FOXM1 deletion/WT.