Fig. 8

Gene expressions associated with TAD A/B compartment switches. A A total of 30,539, 25,335, and 29,647 A compartments (open state) were identified in ATC, PTC, and normal cells, respectively; a total of 26,420, 31,614, and 27,314 B compartments (closed state) were identified in ATC, PTC, and normal cells, respectively. B By comparing ATC with normal cells, a total of 0.6% genomic regions switched from compartment A (open state) in normal cells to compartment B in ATC and were associated with downregulated gene expression. In contrast, 0.9% of genomic regions exhibited the opposite switching from compartment B in normal cells to compartment A in ATC and were associated with upregulated gene expression. C, D Compared with normal cells, a total of 3562 genes (1727 downregulated and 1835 upregulated genes) and 2786 genes (1308 downregulated and 1478 upregulated genes) were differentially expressed in ATC and PTC, respectively. E–F GO and pathway enrichment analysis for genes switched E from compartment A to B, or F from compartment B to A. G Overall study scheme