Fig. 6 (draft v3 layout; results/182/182_Fig6_v3). HPC. Groups: Alu-near (classes 1 + 5), Alu-mid (2 + 3 + 6), Alu-far (4 + 7), L1/LTR CGI (8 + 9); RP genes excluded.
(A) H3K4me3 (top) and H3K27me3 (bottom) signal around the TSS, even-numbered autosomes (n = 3,986 / 920 / 169 / 708 genes); mean signal in 100-bp bins; bands, gene-level bootstrap 95% intervals (1,000 draws); separate y scales; the x axis is shared with B.
(B) CpG methylation around the TSS. CpGs overlapping RepeatMasker elements excluded; 100-bp bins measured from the TSS, upstream and downstream kept separate; mean of gene means; bands, gene-level bootstrap 95% intervals (1,000 draws). Dotted line, 50%. Coloured ticks on the x axis, median TSS-to-island-edge distance of each group, upstream and downstream.
(C) Methylation boundary position from the TSS (Kaplan-Meier median of the first 100-bp bin >= 50% with the next informative bin >= 50%, >= 2 non-repeat CpGs per bin; sides without a rise within 5 kb are censored at their last informative bin; all autosomes, genes measured in Corces) by group and expression tertile, with gene-clustered 95% intervals (Data S2, Table 3). The three tertile points of each group are joined by a thin line. Open symbol, fewer than 30 sides (Alu-far top tertile, 28 sides); its upper 95% limit is not reached within 5 kb and the interval is drawn to the axis limit (arrow).
Layout only: no value differs from results/177, 180, 181 and 182 (the dot-plot values are results/181 Table 3, HPC).
