Figure 2.

CIS gene signature and pathway analysis

(A) Gene signature categorizing samples into luminal, ECM and smooth muscle, EMT and claudin, basal, squamous, Immune, neuronal differentiation, CIS surrounding, and Sonic hedgehog markers.

(B) Composite signature scores shown as boxplots for CIS and tumor samples (Wilcoxon rank-sum test derived p-value shown) (C) Differentially expressed hallmark pathways specific to CIS tumors. Upregulated and downregulated pathways are shown in red and blue, respectively.