Fig. 6 (draft v5; results/182/182_Fig6_v5). Groups (RP genes excluded): Alu-near (classes 1 + 5), Alu-mid (classes 2 + 3 + 6), Alu-far (classes 4 + 7), L1/LTR CGI (classes 8 + 9).
(A) Promoter profiles in HPC, T cells and B cells, even-numbered autosomes (HPC panels: n = 3,986 /   920 /   169 /   708 genes for Alu-near / Alu-mid / Alu-far / L1/LTR CGI): H3K4me3 and H3K27me3 signal and CpG methylation from 2.5 kb upstream to 2.5 kb downstream of the TSS (strand-oriented, 100-bp bins). Histone signal scales differ between cell types (each cell type has its own y scale) and are not compared across cell types; methylation is on one 0-85% axis. CpGs overlapping RepeatMasker elements are excluded; methylation is the gene-level mean per bin, then the mean over genes. Bands, gene-level bootstrap 95% intervals (1,000 draws). Coloured ticks on the methylation axis, median TSS-to-island-edge distance of each group (upstream and downstream); grey line, 50%.
(B) Methylation boundary by expression in HPC only (the T- and B-cell versions are in Fig. S8). Boundary (rise) = the first 100-bp bin from the TSS with >= 2 non-repeat CpGs whose mean methylation is >= 50% and whose next informative bin is also >= 50%; sides whose informative CpGs end before a rise are censored there. Curves, Kaplan-Meier fraction of sides risen by distance from the TSS (gene-clustered; the 95% intervals of the medians are in Data S2, Table 3) in the expression tertiles of each group (bottom light, middle, top full colour; tertiles from Corces TPM within HPC, genes measured in Corces, all autosomes); ticks on the x axis, tertile KM medians; grey line, 0.5. Thin line with n, fewer than 50 sides.
Layout only: no value differs from results/177, 180, 181 and 182.
