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Supplementary Figure Legends:
Figure S1: Comparison of lung cancer and pan-cancer EMT signatures for correlation with
known markers of EMT. (A) A total of 14 genes are shared between the EMT signatures,
including AXL. (B) Pan-cancer EMT signature improves correlation with known markers of EMT,
including miR-200 family members across tumor types.
Figure S2: EMT gene expression and pathway analysis. (A) Word cloud for genes correlated
with EMT score. Correlation gap (defined in methods) was used to group the genes in different
sectors. Text size is proportional to correlation gap; red is mesenchymal-like; blue is epitheliallike. (B) Correlation gap (weakest correlation across all tumors) of gene expression across
different tumor types. Genes both positively and negatively correlated with EMT across tumor
types are represented by a correlation gap of zero. (C) Correlation of example (top 50) genes
with EMT score. Actionable genes such as AXL and PDGFR rank in the top list and show strong
correlation with EMT score across tumors. Overall, stronger correlation is observed in genes
associated with mesenchymal status (red) than those associated with epithelial status (blue).
(D) Pathway analysis of commonly expressed genes in all tumor types. AXL and known EMT
regulators TWIST and ZEB are involved in the top network derived from this model.
Figure S3: miRNA correlation with EMT score. (A) A number of miRNAs are positively
correlated with the pan-cancer EMT score, including miR-199a (left). Although fewer miRNAs
are consistently inversely correlated with EMT, miR-200 family expression is associated with
epithelial scores (right). (B) miR-200 family mRNA targets are not uniformly distributed (P <
0.001), with more targets being ranked in the top 20% of mRNAs positively correlated with the
pan-cancer EMT score.
Figure S4: Mutational landscape in mesenchymal tumors. (A) Driver genes significantly
correlated (adjusted P value < 0.05) with the pan-cancer EMT score. (B) Driver genes with at
least a 2% mutation rate (1,073) and with a Q value < 0.1 in at least one of the cancers by
Mutsig CV analysis were correlated with the pan-cancer EMT score. Genes with a raw P value <
0.001 are shown by tumor type. (C) Mutation and copy number alteration burden is not
influenced by EMT status.
Figure S5: Association of EMT and tumor grade. As tumor grade increases in (A) head and neck
squamous cancer (HNSC) and KIRC (b), the EMT score increases (P = 4.5*10-8 and P = 0.01,
respectively).
Figure S6: Potential therapeutic targets in mesenchymal tumors (GDSC target analysis).
Targets are shown in regard to increased sensitivity (green) or resistance (red) to therapy in
mesenchymal cell lines derived from different tumor