Fig. 4

GNT analysis of TCGA RNA sequencing experiments. a Summary of the GNT results on the TCGA datasets. For each geneset analysed, a summary of all test results is reported. In order to make results comparable, observed test statistics are transformed in normalised z-scores. All results are in a scatter plot, where significant tests are marked with a red dot. We can notice that only the TCGA Lung Squamous Cell Carcinoma geneset is significant for all topology tests. b Null empirical distribution (blue) and observed value (red bar) for a significant rwr test on the TCGA Lung Squamous Cell Carcinoma geneset. c Barplot of the GNT module analysis on all TCGA datasets. For each geneset, we report both the observed statistic and the empirical null distribution average. Stars are used to identify significance of the test. Here, DLBC (p-value:\(6.99 \times 10^{-3}\)) and LUSC (p-value: \(8.99 \times 10^{-3}\)) are significant, while the other terms are not