Fig. 6 (draft v6; results/182/182_Fig6_v6). Groups (RP genes excluded): Alu-near (classes 1 + 5), Alu-mid (classes 2 + 3 + 6), Alu-far (classes 4 + 7), L1/LTR (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): 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 is shown relative to the mean of all CpG-island promoters in the same cell type (±2.5 kb); methylation is absolute. The relative signal is the profile value divided by the mean signal over TSS ±2.5 kb of the four groups pooled (5,783 genes): H3K4me3, HPC 26.31, T cell 51.24, B cell 35.33; H3K27me3, HPC 2.67, T cell 1.02, B cell 0.94 (signal units of each data set); the same divisor is applied to the bootstrap bands, one y axis is shared by the three cell types in each histone row, and the dotted line marks 1. Relative scales are not a comparison of absolute signal between cell types. CpGs overlapping RepeatMasker elements are excluded; methylation is the gene-level mean per bin, then the mean over genes, on a common 0-100% axis. 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.
Display scaling only: the underlying values are those of results/177, 180, 181 and 182.
