Fig. 1: Branched-chain amino acid catabolism is suppressed in KIRC.

a Dot plot showing the enriched pathways ranked by significance in KIRC tumors compared to renal healthy tissue obtained through GSEA analysis of RNA-seq data from TCGA. The dot size represents the significance expressed as –log₁₀(p-value). red dots = upregulated pathways, blue dots = downregulated pathways. NES normalized enrichment score. Statistics was calculated using moderated two-sided Student test, p-values were corrected with Benjamini–Hochberg procedure. b Volcano plot showing the differential expression of genes that belong to KEGG “Valine leucine and isoleucine degradation” signature in KIRC tumors compared to renal healthy tissue. FC fold-change, red = upregulated genes, blue = downregulated genes. c Dot plot of the differentially enriched pathways in KIRC tumors comparing stage III/IV vs. stage I/II. Pathways, ranked by significance, are obtained through GSEA analysis of TCGA RNA-seq data. The dot size represents the significance expressed as –log₁₀(p-value). red dots = upregulated pathways, blue dots = downregulated pathways. NES normalized enrichment score. Statistics was calculated using moderated two-sided Student test, p-values were corrected with Benjamini–Hochberg procedure. d Overall survival of KIRC patients obtained through GEPIA, based on gene expression of KEGG ‘Valine, leucine and isoleucine degradation’ signature. Cut-off used for high/low groups was 50% and p-value displayed as –logrank(p-value) calculated using Mantel–Cox test. The dotted line refers to the survival with a confidence interval (CI) of 95%. n number of samples compared, HR = hazard ratio based on the Cox PH model. KIRC = Renal clear cell carcinoma.