Fig. 5

Tumor gene signature is predictive of survival and associated with copy number variations. A Tumor gene signature genes are more likely to be significantly prognostic for patient survival in at least one cancer type (enrichment p value was lower than 0.01, as determined by a chi-square test). Data was extracted from the protein atlas. B The association of tumor gene signature genes with poor survival outcomes is evident in multiple cancer types. p values for within cancer comparisons are reported in Additional File 3: Statistics. C Data from [52] show that the tumor gene signature genes have much higher Stoufer’s z (association with poor survival outcomes) than rest of protein coding genes (p value was lower than 0.01, based on the Wilcoxon rank-sum test). D Increased association of the tumor signature genes with negative survival is apparent in 23 out of 33 cancer types (the BH-FDR adjusted p value was lower than 0.01 as determined by Wilcoxon rank-sum test). E Genes from the tumor gene signature are more likely to participate in 3′ or 5′ fusions. When compared to sets of randomly drawn genes, the tumor signature genes had a significantly higher probability of participating in genomic fusions. The red vertical line depicts the overlap of the tumor signature list with the corresponding gene fusion list (the BH-FDR adjusted p value was lower than 0.01, as determined by the resampling test). F Genes from the tumor gene signature are frequently found in amplified or deleted genomic regions. We have measured the percentage of the gene list which overlaps with the known CNV regions for each cell line in the CCLE dataset. The tumor gene signature was found to be enriched in 22/27 cancer types (BH-FDR adjusted empirical p value was lower than 0.01 based on resampling tests). Background distributions were derived from expression matched randomly sampled gene lists