Fig. 5: Global transcriptomic effects of SOX2OE in mutant hBECs.
From: A human model to deconvolve genotype-phenotype causations in lung squamous cell carcinoma
a Strategy for the identification of processes associated with each single pathway (TC + S/K/P) and all pathways in combination (TC + PKS). Gene expression changes associated with the dysregulation of each single pathway and all pathways in combination were identified by carrying out differential gene expression (TC + P/S/K/PKS versus TC) followed by gene set enrichment analysis (GSEA). b Clustergram of significant positively enriched gene ontologies (Biological Process) using GSEA of genes differentially expressed in TC + S versus TC comparisons (q-value ≤ 0.05). Terms were aggregated by semantic similarity using the simplifyEnrichment package. c GSEA plots showing the significant positive enrichment (q-value < 0.05) of the KRAS signalling up hallmark (MSigDB, H: hallmark gene sets) in genes differentially expressed in TC + S versus TC (q-value ≤ 0.05). d Heatmap showing the normalised expression of EGFR ligands across the entire sample set. e Dot plot showing positively enriched gene ontologies related to protein degradation within the ‘protein modification and degradation’ cluster from (b). GO:0010466=negative regulation of peptidase activity, GO:0045861=negative regulation of proteolysis, GO:0052547=regulation of peptidase activity. f Plot showing the expression of PI3 in normal (n = 42), low (n = 41) and high-grade (n = 25) premalignant lesions and LUSC (n = 14). Significance was calculated by comparing each group to ‘normal’ using the two-sided Mann-Whitney test. GEO accession: GSE33479. g Clustergram of significant (q-value < 0.05) negatively enriched gene ontologies (Biological Process) using GSEA of genes differentially expressed in TC + S versus TC comparisons (q-value ≤ 0.05). h Dot plot showing negatively enriched gene ontology terms related to MHC-II peptide presentation within the ‘protein transport and complex assembly’ cluster from (g). GO:0019886=antigen processing and presentation of exogenous peptide antigen via MHC class II, GO:0002478=antigen processing and presentation of endogenous peptide antigen, and GO:0002501=peptide antigen assembly with MHC protein complex. i Heatmap showing the normalised expression of genes involved in MHC-II antigen processing and presentation across the entire sample set. Source data are provided as a Source Data file.
