Fig. 4: Poor prognostic cases were clustered in a specific site of the comparative transcriptome atlas, named Cluster X.

a t-SNE plot colored by five clusters is shown. t-SNE plot in Fig. 3b was used. b Kaplan–Meier curves show the overall survival of patients in five clusters. Log-rank test was used for overall comparisons among clusters. The number of patients in each subgroup was as follows: Chromophobe/Oncocytic type (n = 49), Clear cell type (n = 40), Papillary type (n = 50), Other type (n = 34), and Cluster X (n = 22). c Gene set enrichment analysis (GSEA) results using Hallmark gene sets comparing Cluster X with Clear cell type (left panel), or Cluster X with Papillary type (right panel) are shown. Red triangles indicate pathways associated with tumor progression, yellow triangles indicate immune-related pathways, and blue triangles indicate pathways typically upregulated in Clear cell or Papillary types. d Differentially expressed genes between Cluster X and Clear cell type (left panel), or Cluster X and Papillary type (right panel) are shown. Genes highlighted in black and blue are associated with neural development and the development of other organs, respectively. Statistical differences were assessed using a two-sided Wald test, and p values were adjusted for multiple comparisons using the Benjamini–Hochberg method. The number of patients in each subgroup was as follows: Cluster X (n = 24), Clear cell type (n = 53), and Papillary type (n = 56). e A box plot shows signature scores based on the top 20 genes commonly upregulated in Cluster X compared to Clear cell and Papillary types. Gene list is provided in Supplementary Fig. 7a. Statistical differences between groups were assessed using two-sided Wilcoxon rank-sum tests (Cluster X versus each other cluster), and p values were adjusted for multiple comparisons using the Benjamini–Hochberg method. The number of patients in each subgroup was as follows: Chromophobe/Oncocytic type (n = 51), Other type (n = 35), Papillary type (n = 56), Cluster X (n = 24), and Clear cell type (n = 53). Box plots include center line, median; box limits, upper and lower quartiles; whiskers are the highest and lowest values no greater than 1.5 × IQR. f Kaplan–Meier curves show the overall survival of patients in the TCGA cohort grouped according to the median signature score. Log-rank test was used. The number of patients was as follows: 518 for KIRC (n = 262 with a high Cluster X score and n = 256 with a low Cluster X score); 278 for KIRP (n = 139 with a high Cluster X score and n = 139 with a low Cluster X score); and 65 for KICH (n = 32 with a high Cluster X score and n = 33 with a low Cluster X score). Source data are provided in the Source data file.