Fig. 2

Differentially active domains. a Number of differentially active domains identified (X-axis) for all comparisons (Y-axis), ranked by decreasing number. For each comparison, we report the ID of the Hi-C dataset, mRNA expression dataset, and conditions being compared. The fraction of domains comprising any of the top 100 differentially expressed genes is shown in red (in gray otherwise). b Number of differentially active domains (Y-axis) in the observed (blue, left) and random data (gray, right). c Percentage of differentially expressed genes (Y-axis) and differentially active domains (X-axis) in each comparison. The size of the dot is proportional to the number of samples available for the analysis and the color of the dot indicates the category of comparison. d Percentage of differentially expressed genes (dashed-lines) and differentially active domains (solid lines) across different levels of sub-sampling (X-axis) for 3 selected datasets (color coded). e Domain mean gene expression fold-change (X-axis) and domain mean gene expression correlation (Y-axis) for the comparison between KRAS-mutant and EGFR-mutant lung adenocarcinoma (LUAD) (Hi-C data from the lung cancer cell line NCI-H460). Size of the dot is proportional to significance of the chromatin domain, blue (red) indicates negative (positive) average fold-change. Highlighted are two chromatin domains (CD) selected as a case study (chr10-CD16 and chr17-CD162). f Boxplot comparison of mRNA expression values (log10) for the genes belonging to chr10-CD16. KRAS mutant samples are color coded based on whether they also exhibit either NFE2L2 (NRF2) or KEAP1 mutations (yellow) or not (blue). EGFR mutant samples are in gray. g Top line represents the gene ranks based on differential expression analysis. Bottom line represents rank of the domain obtained from DADo. Genes from chr10-CD16 are shown in red. h Boxplot comparison of mRNA expression values (log10) for the genes belonging chr17-CD162. EGFR mutant samples are in red KRAS mutant samples are in gray. i Top line represents the gene ranks based on differential expression analysis. Bottom line represents rank of the domain obtained from DADo. Genes chr17-CD162 are shown in red.