FIGURE 3.

Lung squamous cell carcinoma (SCC) consensus subtypes independent validation. (A) New CPTAC‐3 lung SCC samples were mapped on the previously established classification of SCC tumours based on the activity levels of the same 50 pathways used to define the original SCC subtypes. The new sample subtype status was decided based on the most frequent label of the closest neighbours of the original classification. Coloured circles represent samples used in the original set, whereas triangles represent new CPTAC‐3 validation set samples. (B) Copy number burden across newly classified CPTAC‐3 lung SCC samples. Each dot represents the number of altered genes per sample. The Kruskal‐Wallis test was used to make comparisons between groups. p‐Value was corrected using the false discovery rate (FDR) multiple‐comparisons correction method. (C) Relative activity levels of the 50 studied pathways in each of the 108 CPTAC‐3 lung SCC samples were assigned to a consensus subtype. Red colours indicate higher relative activity of a pathway in a certain sample, whereas blue colours indicate lower relative activity of a pathway in a certain sample.