Fig. 5: Copy number and protein level differences between SCC subgroups.

a 3 copy number amplifications (red points) and 2 copy number deletions (blue points) were significantly enriched (Wald Test, FDR < 0.05, horizontal dotted line) in C2 tumours as determined by binomial regression. GISTIC copy number peak frequencies between C1 and C2 tumours, also had to have a log2 odds ratio (x axis) >1 or <−1 (vertical dotted lines) to be considered as enriched in either cluster. b Using reverse phase protein array data for 140 CSCCs in the TCGA cohort 18 proteins are differentially expressed between C1 and C2, 7 proteins upregulated in C2 and 11 upregulated in C1 tumours. Orange points represent proteins that are expressed at a fold change of >1.3 or a fold change < 1.3 and where the FDR is <0.05 (t-test). Source data are provided as a Source Data file.