Fig. 6 (draft v2 layout; results/182/182_Fig6_v2). 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) CpG methylation around the TSS, even-numbered autosomes (n = 3,986 / 920 / 169 / 708 genes). 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.
(B) Methylation boundary on each island side: Kaplan-Meier fraction of sides whose methylation has risen (first 100-bp bin >= 50% with the next informative bin >= 50%, >= 2 non-repeat CpGs per bin), by distance from the TSS; sides without a rise within 5 kb are censored at their last informative bin. All autosomes, genes measured in Corces. Lines, expression tertiles (bottom light, middle, top full colour); ticks on the x axis, tertile KM medians (as in C); dotted line, median TSS-to-edge distance; dashed line, median TSS-to-nearest-retroelement distance (Alu, L1 or LTR; not shown when > 5 kb). Thin line with n, fewer than 50 sides.
(C) KM median boundary position from the TSS by group and expression tertile with gene-clustered 95% intervals (Data S2, Table 3); open symbol, fewer than 30 sides; the Alu-far top-tertile upper limit is not reached and is drawn to the axis limit.
