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. 2022 Nov 5;13:6689. doi: 10.1038/s41467-022-34514-z

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© The Author(s) 2022, corrected publication 2022

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Fig. 5 — A UpSet R plot showing the hyper- and hypo-methylated CpGs sites (DMCs) in RELA (upper panel) and PFA (lower panel) primary tumors (-P) as compared with normal cerebrum or cerebellum tissues. The horizonal histogram represents the number of DMCs in each comparison between primary tumor and normal brain tissues; the vertical histogram represents the number of DMCs shared by tumors marked by connected dots. Red and green bar highlights the hyper- and hypoDMCs that were shared by all the tumors that eventually recurred (primary-tumor^{Eventually recurred}) but not in the normal brain tissues and the non-recurrent reference tumors. B Bar graph showing the frequencies of hyper- and hypoDMCs specific to ependymoma primary tumors that eventually recurred (-P-Specific) and that did not relapse (-NonRecur Specific) in the RELA recurrent (n = 12) and PFA (n = 10) recurrent tumors. Boxplots indicate median, first and third quartiles (Q1 and Q3), whiskers extend to the furthest values; the uppermost and lowest line indicates the maximum and minimum values, respectively. In RELA tumors, the numbers of HyperDMCs analyzed are RELA6- NonRecurSpecific (n = 10,309 CpGs), RELA-P-specific (n = 357,141 CpGs); wherease of the HypoDMCs are RELA6-NonRecurSpecific (n = 17,188 CpGs) and RELA-P-specific (n = 507,987 CpGs). In PFA tumors, the HyperDMCs analyzed are PFA6-NonRecurSpecific (n = 24,296 CpGs) and PFA-P-specific (n = 349,746 CpGs); and HypoDMCs PFA6NonRecurSpecific (n = 40,525 CpGs); PFA-P-specific (n = 451,426 CpGs). C Heatmap showing the DNA methylation ratios of DMCs specific to RELA (upper panel) or PFA (lower panel) primary tumors^{Eventually recurred} exist in all recurrent tumors. Black dash box shows that these DMCs have similar DNA methylation ratios among RELA-/PFA-NonRecur primary tumor, normal cerebellum and cerebrum, but different from the primary tumors Eventually recurred. D Venn diagram representing the number of overlapped and specific hyper/hypoDMCs (from C) between RELA and PFA. E Heatmap showing the top CpGs’ DNA methylation ratios with highest confidence that can potentially predict recurrence from primary tumors of RELA (upper panel) and PFA (lower panel) ependymoma.