Fig. 2

Multi-omics landscape of cuproptosis genes across ccRCC in TCGA cohort. A Circos plot shows the chromosome positions of cuproptosis genes. B Transcriptome profiling of cuproptosis genes in ccRCC versus normal specimens. Colors from blue to red denote low to high expression. C Comparison of cuproptosis genes in paired ccRCC and normal specimens. The center line indicates the median, and the upper and lower lines indicate the upper and lower quartiles. D Interactions between cuproptosis genes at the transcriptional level. Blue line, negative correlation; red line, positive correlation. E Methylation profiling of cuproptosis genes in ccRCC versus normal specimens. Colors from blue to red indicate low to high methylation. F Frequencies of copy number amplification and deletion of cuproptosis genes in ccRCC. Blue dot, amplification; yellow dot, deletion. G K-M curves for OS between groups separated by the median expression value of each cuproptosis gene. H PCA plots illustrate the discrimination of transcriptome profiling of cuproptosis genes between ccRCC and normal samples. Each dot denotes a sample. Blue dot, normal tissue; yellow dot, ccRCC tissue. I Associations of cuproptosis genes with 22 tumor-infiltrating immune cell types and two stromal cells within the tumor microenvironment. Colors from blue to red denote negative to positive correlation. J, K Comparison of the transcription levels of CDKN2A between groups separated by grade and stage. Each point indicates a sample; the center line indicates the median, and the upper and lower lines indicate the upper and lower quartiles. L GSEA shows the GO terms with significance differences between low and high CDKN2A expression groups. For asterisks, ns: p-value > 0.05; *p < 0.05; **p < 0.01; ***p < 0.001