Fig. 7

Suppressed immune phenotype in ARNT- and ERBB2-altered NMIBC patients. A Boxplots comparing ARNT-altered versus wild-type samples with Mann-Whitney p-values noted beneath. The first three boxplots are for the interleukin receptor genes. The fourth boxplot compares the median expression of the Gene Ontology gene set (GO: 0004907) for interleukin receptor activity. The fifth boxplot compares the ConsensusTME-derived immune score. B Boxplots comparing ERBB2-altered versus wild-type samples with Mann-Whitney p-values noted beneath. The first and second boxplots compare the TLK2 and CD151 gene expression, respectively. The third boxplot compares the ConsensusTME-derived immune score. C, E Kaplan-Meier plot comparing the progression-free survival (PFS) with ARNT (C) or ERBB2 (E) expression level. The third quartile from the distribution of respective expression values (n = 74) was taken as the cut-off to assign “ARNT-High”/“ERBB2-High”, or “ARNT-Low”/“ERBB2-Low” samples. The depicted p-values are from the log-rank test. D, F The top three pathways from the gene set enrichment analysis (GSEA) in ARNT- (D) and ERBB2-altered (F) samples, respectively. “NES” is the normalised enrichment score, and the negative sign here indicates that the enrichment was found amongst the downregulated genes