Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development

Liang, Ping; Song, Fei; Ghosh, Srimoyee; Morien, Evan; Qin, Maochun; Mahmood, Saleh; Fujiwara, Kyoko; Igarashi, Jun; Nagase, Hiroki; Held, William A

doi:10.1186/1471-2164-12-231

BMC Genomics

Table 2 The number of DS-DMRs in different tissues

From: Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development

	Total	Adjusted^#	%¹	CpGi-Prom	%²	non-CpGi-Prom	%²	Intra-genic CpGi	%²	Inter-genic CpGi	%²
Brain:
Common	1903	NA	ND	182	9.6	1018	53.5	493	25.9	210	11.0
E15_uniq	533	533	27.5	105	19.7	359	67.4	35	6.6	34	6.4
E15+NB	490	509	25.3	66	13.5	368	75.1	29	5.9	27	5.5
NB_uniq	370	400	19.1	55	14.9	248	67.0	42	11.4	25	6.8
AD_uniq	408	532	21.1	94	23.0	233	57.1	52	12.7	29	7.1
NB+AD	70	82	3.6	5	7.1	40	57.1	16	22.9	9	12.9
E15+AD	65	77	3.4	11	16.9	46	70.8	7	10.8	1	1.5
Total*	1936	2132	100.0	336	15.2	1294	62.6	181	13.9	125	8.4
UnMe-AD**	1393	1442	72.0	226	16.2	975	70.0	106	7.6	86	6.2
Me-AD***	543	691	28.0	110	20.3	319	58.8	75	13.8	39	7.2
Heart:
Common	1844	NA	ND	218	11.8	946	51.3	491	26.6	189	10.2
E15_uniq	46	81	6.9	27	58.7	8	17.4	2	4.3	9	19.6
E15+NB	87	125	13.0	17	19.5	61	70.1	4	4.6	5	5.7
NB_uniq	93	112	13.9	12	12.9	64	68.8	7	7.5	10	10.8
AD_uniq	172	172	25.6	45	26.2	83	48.3	33	19.2	11	6.4
NB+AD	246	253	36.7	44	17.9	132	53.7	54	22.0	16	6.5
E15+AD	27	34	4.0	6	22.2	15	55.6	5	18.5	1	3.7
Total*	671	777	100.0	151	22.4	363	54.1	105	15.6	52	7.7
UnMe-AD**	226	318	33.7	56	24.8	133	58.8	13	5.8	24	10.6
Me-AD***	445	459	66.3	95	21.3	230	51.7	92	20.7	28	6.3
Liver:
Common	1497	NA	ND	141	9.4	726	48.5	425	28.4	205	13.7
E15_uniq	117	119	4.9	25	21.4	74	63.2	10	8.5	8	6.8
E15+NB	1419	1431	60.0	198	14.0	1034	72.9	125	8.8	62	4.4
NB_uniq	147	147	6.2	24	16.3	109	74.1	8	5.4	6	4.1
AD_uniq	468	813	19.7	70	15.0	322	68.8	45	9.6	31	6.6
NB+AD	36	46	1.5	2	5.6	30	83.3	3	8.3	1	2.8
E15+AD	194	249	8.1	13	6.7	130	67.0	31	16.0	20	10.3
Total*	2381	2804	100.0	332	13.9	1699	71.4	222	9.3	128	5.4
UnMe-AD**	1683	1696	70.7	247	14.7	1217	72.3	143	8.5	76	4.5
Me AD***	698	1107	29.3	85	12.	482	69.1	79	11.3	52	7.4
Testis:
Common	570	NA	ND	20	3.5	363	63.7	148	26.0	39	6.8
E15_uniq	272	380	6.3	105	38.6	101	37.1	33	12.1	33	12.1
E15+NB	939	1094	22.0	193	20.6	480	51.1	157	16.7	109	11.6
NB_uniq	798	789	18.4	231	28.9	391	49.0	86	10.8	90	11.3
AD_uniq	2214	2336	50.9	71	3.2	1908	86.2	165	7.5	70	3.2
NB+AD	63	65	1.4	3	4.8	48	76.2	9	14.3	3	4.8
E15+AD	62	91	1.4	5	8.1	38	61.3	14	22.6	5	8.1
Total	4348	4755	100.0	608	14.0	2966	68.2	464	10.7	310	7.1
UnMe-AD**	2009	2263	40.8	529	26.3	972	48.4	276	13.7	232	11.5
Me-AD***	2339	2493	47.6	79	3.4	1994	85.3	188	8.0	78	3.3
Grand Total:
Common	5814	NA	ND	561	9.6	3053	52.5	1557	26.8	643	11.1
DS-DMRs	9336	10469	100.0	1427	15.3	6322	67.7	972	10.4	615	6.6
UnMe-AD**	5311	5719	56.9	1058	19.9	3297	62.1	538	10.1	418	7.9
Me-AD***	4025	4750	43.1	369	9.2	3025	75.2	434	10.8	197	4.9

%¹: percentage is based on the row total vs. total DMRs; %²: percentage is based on the total of DMRs in the row; Total*: Stage specific; UnMe-AD**: unmethylated in AD but methylated in E15 and/or NB; Me-AD***: methylated in Adult but unmethylated in E15 and/or NB; Adjusted#: number of DMRs adjusted based on the adjusted coefficiency between the duplicated samples.

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com