Fig. 3

Transcriptomic and epigenetic alterations uncovered pathological pathways. a A volcano plot of the gene expression changes between group I (GI) and group II (GII). Genes with adjusted p-value less to 0.05 were defined as DEGs. b Functional enrichment of GII-specific (left) and GI-specific (right) genes. c A heatmap of the H3K27ac signals in group-specific peaks. The data were represented as row-normalized z-scores; each row represented a group-specific peaks, and each column represented a LUAD sample. d Genes ranked based on the correlation of gene expression and PC1 in hyper-variable peaks in tumor samples. The purple and orange bars (bottom) indicate GII-specific and GI-specific distal enhancers or SEs linked genes, respectively. e The convergence of GII-specific distal enhancers on cell cycle genes. f Comparison of ssGSEA-score of cell cycle pathway genes and embryonic stem cell core genes between GI and GII, t-test was performed between two different groups. g DEGs between GI and GII were used to group TCGA samples into GI-like, GII-like, and intermediate groups, and the K-M plot of patients’ survival in three groups, p-value determined by log rank test. ***p < 0.001. h The K-M plot of patients’ survival in GI-like and GII-like LUAD patients in stage I and stage II-IV, p-value determined by log rank test. *p < 0.05. i The distribution of GI-like, GII-like and intermediate samples across different tumor stages in the TCGA samples. j Top 30 bias somatic coding mutations in GI-like and GII-like LUAD patients. The middle panel showed somatic mutation by individuals (column) and by genes (row). The histogram on the top showed the number of mutations in each sample. The histogram on the right showed the differences in mutation frequency between GI-like and GII-like LUAD patients. Genes sorted by the p-value of Fisher-exact test