Fig. 4

Integrative RNA and methylation analyses of T-LUAD and T-LUSC versus their control counterparts. a Pathway enrichment analyses on the DEGs of the T-LUAD versus LUAD comparison. b Pathway enrichment analyses on the DEGs of the T-LUSC versus de novo LUSC comparison. c Scatter plots showing differentially expressed genes exhibiting differential methylation levels in T-LUSC versus de novo LUSC comparison, grouped by pathways of interest. Significantly differentially expressed (q value < 0.05 and [beta] >  = log2(1.2)) and methylated (FDR < 0.05 and differential methylation level greater than 0.1) sites are highlighted. Those genes where increased gene body or promoter methylation is correlated with expression positively and negatively, respectively, are labeled