Figure 3. Inactivation Events of TSGs with Cis- and Trans-Effects.

(A) Evaluation of TSG × cancer inactivation events using transcriptomic data. In each panel, the group labeled “high” indicates the significant TSG × cancer events (p_sample < 0.05 and p_gene < 0.05), and the group “low” indicates non-significant events. Cis- and trans-effects were assessed for L1 mutations and L2 mutations, respectively.

(B and C) MAP3K1 (B) and GATA3 (C) as example genes that had no cis-effect but had a trans-effect. In both cases, as shown, although MAP3K1 and GATA3 were both found with inactivation mutations, their mRNA expression level was not decreased compared to the WT samples of the corresponding genes.

(D) Plot of all TSGs for their cis- and trans-effects. Each dot indicates a TSG × cancer event. Node color indicates the events with different cis- or trans-effects. Nodes with a black circle indicate the 161 events with significant impact.

(E) Distribution of DEGs (y axis) versus T (see main text for the definition of T). Each dot represents a TSG × cancer event. Node color indicates cancer types (like in F), and node size is proportional to the number of inactivated samples.

(F) Distribution of differentially expressed genes (DEGs, y axis) versus empirical p_emp (x axis) of each TSG in each cancer type. Color for cancer types are the same as those in (E).

(G) Distribution of significant DEGs.