Fig. 2

T-cell related gene expression and EMT-related gene expression are positively correlated in UC specimens. a Pathways ranked by their correlation with ITA. Pearson’s correlation coefficient (CC) with ITA was calculated for each individual gene in TCGA UC datasets. Wilcoxon rank sum test was then used to compare CC values in each pathway with all the other genes. X-axis shows the –log10 p-value of the Wilcoxon test for each pathway (pathways that were negatively correlated with ITA were given log10 p-value instead); b Plot of the correlation between ITA and EMT in TCGA UC samples; c Plot EMT-related gene expression for different molecular subtypes of UC in TCGA; d Plot EMT-related gene expression for different molecular subtypes of UC in TCGA. For boxplots, boxes extend from the first to third quartiles, middle line shows median, whiskers extend to the most extreme data point which is no more than 1.5 times the interquartile range from the box, open circles show individual values that are more than 1.5 times the interquartile range from the box