Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation

Table 1 Summary of methylation vs expression changes across feature types

Feature	Meth. type	Direction	N	N unique C	N unique features	Mean N Meth. > 0	Mean N Meth. < 1	Mean Expr change	Prop. age confounded FDR ≥ 5%	Prop. in promoter	Prop. in gene body	Prop. in gene flanking	Prop. CHG	Prop. CHH	Prop. DE glia	Prop. DE neuron	Prop. No Diff
Gene	CpG	Down	18,458	18,353	2074	21.9	21.9	1.39	0.0932	0.0671	0.966	0.906	0	0	0.126	0.329	0.546
	CpG	Up	5217	5021	1743	21.8	21.8	1.69	0.0845	0.0571	0.979	0.92	0	0	0.304	0.193	0.503
	CpH	Down	25,812	25,712	1611	21.1	21.1	1.4	0.115	0.0161	0.519	0.75	0.22	0.781	0.0912	0.413	0.496
	CpH	Up	3842	3840	846	20.1	20.1	1.66	0.2	0.0219	0.532	0.807	0.26	0.744	0.123	0.27	0.607
Exon	CpG	Down	9505	4536	4168	21.9	21.9	1.23	0.104	0.19	0.934	0.991	0	0	0.0097	0.0256	0.965
	CpG	Up	1328	638	687	21	21	1.93	0.191	0.175	0.928	0.988	0	0	0.0369	0.0136	0.95
	CpH	Down	7874	4082	3458	21.1	21.1	1.72	0.074	0.0328	0.437	0.927	0.19	0.814	0.0086	0.0451	0.946
	CpH	Up	1288	733	962	18.7	18.7	1.94	0.154	0.0435	0.481	0.918	0.28	0.722	0.0031	0.0311	0.966
PSI	CpG	Down	4286	2477	1315	21.7	21.7	0.124	0.0272	0.0434	0.994	0.936	0	0	0.242	0.212	0.547
	CpG	Up	5782	3915	1646	21.8	21.8	0.121	0.0195	0.0398	0.991	0.919	0	0	0.261	0.222	0.517
	CpH	Down	1296	945	489	16.8	16.8	0.447	0.0201	0.0274	0.537	0.676	0.36	0.644	0.187	0.286	0.526
	CpH	Up	875	536	391	16.5	16.5	0.169	0.032	0.0279	0.559	0.775	0.36	0.637	0.194	0.33	0.477

Mean values are shown for the number of samples with β > 0, β < 1, and expression change variables (either ΔPSI or Δlog2(FPKM + 1) for genes and exons). Columns from “Age confounded” are proportions. See Additional file 2: Table S12 for a full description of the variables

ISSN: 1474-760X