Fig. 3

Transcriptomic characterization of KPU tumors. A Principal component analysis on the transcriptome of KP and KPU samples. B Heatmap showing the expression of marker genes for LUAD, LUSC, and SCLC in KP and KPU tumors. C GSEA plot of the curated epithelial-to-mesenchymal transition (EMT) hallmark gene set from MSigDB using RNA-seq data of tumors from KP and KPU mice. D Heatmap showing genes significantly upregulated in the “EMT” gene set from (C). E Enrichment plots of hallmark gene set from MSigDB collection in KP versus KPU type 1 tumors (left) and KP versus KPU type 2 tumors (right) by GSEA analysis. F IPA analysis of RNA-seq data showing the top ten canonical pathways enriched in KPU tumors compared with KP tumors. Each bar's color indicates predicted pathway activation or inhibition; Orange, positive z-score (activation); white, zero z-score; blue, negative z-score (inhibition); gray, no pattern. G Upstream regulator analysis exhibiting the predicted activation status of transcription factors in KPU tumors. A positive z-score indicates activation and a negative z-score indicates inactivation. H Heatmap visualization of IPA upstream regulators altered in KP versus KPU tumors and LUAD versus LUSC patients. The z-score predicts activation (orange) and suppression (blue). I Heatmap to show the LUSC subtypes of KPU tumors by the signature gene sets. Row for samples, columns for LUSC subtypes. Asterisk indicates p < 0.05