Human methylome studies SRP155006 Track Settings
Study title: Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancersSRA: SRP155006 GEO: GSE117593 Pubmed: 30709419
Experiment
Label
Methylation
Coverage
HMRs
HMR size
AMRs
AMR size
PMDs
PMD size
Conversion
Details
SRX4452737 Liver
0.730
3.8
24339
1460.2
448
1155.8
13
385394.1
0.980
title: GSM3304382 Liver_HC_01, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Healthy control", "sex": "male", "age": "55", "body_mass_index": "23"}
SRX4452738 Liver
0.702
4.3
26771
1414.9
1046
1158.3
25
181091.7
0.979
title: GSM3304383 Liver_HC_02, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "bariatric surgery", "diagnosis": "Healthy control", "sex": "female", "age": "67", "body_mass_index": "58.7"}
SRX4452739 Liver
0.724
3.9
25055
1489.7
590
1129.6
54
164063.9
0.983
title: GSM3304384 Liver_HC_03, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "bariatric surgery", "diagnosis": "Healthy control", "sex": "male", "age": "46", "body_mass_index": "42"}
SRX4452740 Liver
0.747
3.6
24284
1437.5
324
1191.2
63
158612.0
0.982
title: GSM3304385 Liver_HC_04, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "bariatric surgery", "diagnosis": "Healthy control", "sex": "female", "age": "44", "body_mass_index": "38"}
SRX4452741 Liver
0.738
4.6
28083
1359.6
1348
20552.8
46
127261.1
0.981
title: GSM3304386 Liver_HC_05, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "bariatric surgery", "diagnosis": "Healthy control", "sex": "male", "age": "57", "body_mass_index": "35"}
SRX4452742 Liver
0.717
4.5
26855
1512.3
1143
16954.0
84
77479.8
0.982
title: GSM3304387 Liver_HC_06, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "bariatric surgery", "diagnosis": "Healthy control", "sex": "female", "age": "23", "body_mass_index": "41"}
SRX4452743 Liver
0.721
3.7
22979
1382.3
471
39337.2
32
125434.3
0.978
title: GSM3304388 Liver_NAFLD_01, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "male", "age": "72", "body_mass_index": "32"}
SRX4452744 Liver
0.725
4.0
25034
1443.8
571
32666.9
70
148488.7
0.982
title: GSM3304389 Liver_NAFLD_02, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "male", "age": "22", "body_mass_index": "35"}
SRX4452745 Liver
0.716
5.1
28101
1290.5
2682
1233.3
67
91041.0
0.980
title: GSM3304390 Liver_NAFLD_03, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "female", "age": "60", "body_mass_index": "51"}
SRX4452746 Liver
0.736
4.7
28335
1302.3
1582
1144.3
76
119444.4
0.982
title: GSM3304391 Liver_NAFLD_04, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "female", "age": "32", "body_mass_index": "46"}
SRX4452747 Liver
0.727
4.0
25038
1388.8
733
1119.1
22
188161.0
0.981
title: GSM3304392 Liver_NAFLD_05, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "female", "age": "52", "body_mass_index": "36"}
SRX4452748 Liver
0.717
4.6
26767
1321.1
1592
12454.6
78
120684.2
0.980
title: GSM3304393 Liver_WD_Hep_01, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "22", "body_mass_index": "30"}
SRX4452749 Liver
0.725
3.6
23691
1489.2
328
56050.5
47
206449.4
0.982
title: GSM3304394 Liver_WD_Hep_02, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "50", "body_mass_index": "32"}
SRX4452750 Liver
0.736
3.5
22805
1434.0
233
1250.9
51
119079.4
0.982
title: GSM3304395 Liver_WD_Hep_03, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "46", "body_mass_index": "34"}
SRX4452751 Liver
0.721
4.0
24656
1413.6
861
22041.5
33
183980.8
0.979
title: GSM3304396 Liver_WD_Hep_04, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "40", "body_mass_index": "28"}
SRX4452752 Liver
0.713
3.7
22975
1443.2
463
1130.0
31
220722.1
0.981
title: GSM3304397 Liver_WD_Hep_05, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "percutaneous biopsy", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "36", "body_mass_index": "34"}
SRX4452753 Liver
0.735
3.5
21292
1394.1
254
1155.2
24
162912.0
0.982
title: GSM3304398 Liver_WD_Hep_06, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "liver transplant", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "45", "body_mass_index": "N/A"}
SRX4452754 Liver
0.725
4.4
24048
1304.4
1266
1125.3
52
92971.3
0.983
title: GSM3304399 Liver_WD_Hep_07, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "liver transplant", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "41", "body_mass_index": "N/A"}
SRX4452755 Liver
0.731
3.7
23284
1383.2
379
1129.4
47
119279.6
0.983
title: GSM3304400 Liver_WD_Hep_08, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "liver transplant", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "31", "body_mass_index": "N/A"}
SRX4452756 Liver
0.723
3.9
23769
1333.2
738
1092.1
69
101777.9
0.983
title: GSM3304401 Liver_WD_Hep_09, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "liver transplant", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "23", "body_mass_index": "N/A"}
SRX4452757 Liver
0.732
3.6
24191
1422.7
355
1087.7
85
155123.1
0.981
title: GSM3304402 Liver_WD_Hep_10, Homo sapiens, Bisulfite-Seq; {"source_name": "liver", "circumstances": "liver transplant", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "38", "body_mass_index": "N/A"}
SRX4452758 Blood
0.745
4.5
30234
1225.6
545
1287.8
74
77255.5
0.971
title: GSM3304403 Blood_HC_01, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "male", "age": "27", "body_mass_index": "22.8"}
SRX4452759 Blood
0.738
4.1
29215
1232.1
359
1230.0
70
110932.6
0.972
title: GSM3304404 Blood_HC_02, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "male", "age": "45", "body_mass_index": "30.5"}
SRX4452760 Blood
0.745
4.1
30233
1218.4
401
1251.5
89
94378.7
0.972
title: GSM3304405 Blood_HC_03, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "male", "age": "28", "body_mass_index": "30.7"}
SRX4452761 Blood
0.748
4.4
32269
1207.3
509
1167.1
170
76609.6
0.972
title: GSM3304406 Blood_HC_04, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "male", "age": "33", "body_mass_index": "26.2"}
SRX4452762 Blood
0.748
4.1
30503
1239.3
380
1380.0
86
76895.6
0.974
title: GSM3304407 Blood_HC_05, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "male", "age": "32", "body_mass_index": "22.8"}
SRX4452763 Blood
0.743
4.4
32090
1196.2
679
1169.0
93
85433.1
0.972
title: GSM3304408 Blood_HC_06, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "female", "age": "38", "body_mass_index": "20.1"}
SRX4452764 Blood
0.737
4.3
30886
1206.8
609
1227.9
113
85867.0
0.967
title: GSM3304409 Blood_HC_07, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "female", "age": "26", "body_mass_index": "19.1"}
SRX4452765 Blood
0.733
4.4
29988
1242.1
727
1235.5
96
77525.5
0.968
title: GSM3304410 Blood_HC_08, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "female", "age": "49", "body_mass_index": "26.4"}
SRX4452766 Blood
0.730
4.0
27691
1274.6
514
1115.3
68
82316.3
0.973
title: GSM3304411 Blood_HC_09, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "female", "age": "27", "body_mass_index": "21.2"}
SRX4452767 Blood
0.743
4.3
32088
1209.9
641
1336.7
85
84124.2
0.971
title: GSM3304412 Blood_HC_10, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "female", "age": "52", "body_mass_index": "23.8"}
SRX4452768 Blood
0.743
4.2
29189
1283.3
342
1350.0
91
99196.2
0.967
title: GSM3304413 Blood_HC_11, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "male", "age": "59", "body_mass_index": "24.6"}
SRX4452769 Blood
0.740
4.1
27931
1246.0
402
1301.6
43
134415.4
0.971
title: GSM3304414 Blood_HC_12, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Healthy control", "sex": "female", "age": "21", "body_mass_index": "24"}
SRX4452770 Blood
0.748
4.1
28646
1253.5
408
1580.3
60
118441.7
0.970
title: GSM3304415 Blood_NAFLD_01, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "female", "age": "52", "body_mass_index": "47.3"}
SRX4452771 Blood
0.741
4.5
31414
1224.7
847
1386.8
158
61675.8
0.971
title: GSM3304416 Blood_NAFLD_02, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "female", "age": "50", "body_mass_index": "38.4"}
SRX4452772 Blood
0.755
4.3
29214
1229.2
615
1256.2
67
96110.5
0.974
title: GSM3304417 Blood_NAFLD_03, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "female", "age": "58", "body_mass_index": "40.7"}
SRX4452773 Blood
0.739
4.3
28699
1259.8
528
1351.1
61
88231.2
0.969
title: GSM3304418 Blood_NAFLD_04, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "male", "age": "43", "body_mass_index": "28.9"}
SRX4452774 Blood
0.755
4.3
27703
1303.1
284
1798.7
62
102881.8
0.964
title: GSM3304419 Blood_NAFLD_05, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "male", "age": "24", "body_mass_index": "39.7"}
SRX4452775 Blood
0.749
4.4
29384
1252.5
403
1331.5
74
94554.2
0.972
title: GSM3304420 Blood_NAFLD_06, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "male", "age": "66", "body_mass_index": "27"}
SRX4452776 Blood
0.732
4.2
27464
1287.9
423
1163.8
45
96326.1
0.973
title: GSM3304421 Blood_NAFLD_07, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "male", "age": "63", "body_mass_index": "29.7"}
SRX4452777 Blood
0.748
4.2
29878
1235.1
485
1301.1
78
88807.2
0.972
title: GSM3304422 Blood_NAFLD_08, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "female", "age": "59", "body_mass_index": "30"}
SRX4452778 Blood
0.750
4.5
32461
1196.6
464
1307.5
93
85092.5
0.972
title: GSM3304423 Blood_NAFLD_09, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "male", "age": "40", "body_mass_index": "28.5"}
SRX4452779 Blood
0.745
4.2
29519
1242.1
501
1341.3
71
98558.6
0.973
title: GSM3304424 Blood_NAFLD_10, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Non-alcoholic fatty liver disease", "sex": "female", "age": "55", "body_mass_index": "26.5"}
SRX4452780 Blood
0.756
4.0
28174
1262.4
324
1213.9
75
111207.4
0.970
title: GSM3304425 Blood_PSC_01, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Primary sclerosing cholangitis", "sex": "female", "age": "53", "body_mass_index": "33"}
SRX4452781 Blood
0.736
4.1
29476
1244.7
566
1441.9
136
85740.3
0.971
title: GSM3304426 Blood_PSC_02, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Primary sclerosing cholangitis", "sex": "female", "age": "23", "body_mass_index": "21.6"}
SRX4452782 Blood
0.725
4.4
29550
1248.4
863
21996.5
56
84279.1
0.968
title: GSM3304427 Blood_PSC_03, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Primary sclerosing cholangitis", "sex": "female", "age": "61", "body_mass_index": "41.4"}
SRX4452783 Blood
0.745
4.0
31257
1232.1
406
1209.6
72
102236.6
0.969
title: GSM3304428 Blood_PSC_04, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Primary sclerosing cholangitis", "sex": "female", "age": "45", "body_mass_index": "27"}
SRX4452784 Blood
0.740
4.4
30982
1220.2
745
1281.3
95
73237.8
0.974
title: GSM3304429 Blood_PSC_05, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Primary sclerosing cholangitis", "sex": "female", "age": "33", "body_mass_index": "29.6"}
SRX4452785 Blood
0.750
4.2
29669
1237.1
374
1238.4
69
98385.2
0.972
title: GSM3304430 Blood_PSC_06, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Primary sclerosing cholangitis", "sex": "male", "age": "63", "body_mass_index": "21.8"}
SRX4452786 Blood
0.747
5.0
32246
1226.4
672
1299.7
118
67265.6
0.967
title: GSM3304431 Blood_PSC_07, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Primary sclerosing cholangitis", "sex": "male", "age": "58", "body_mass_index": "31.4"}
SRX4452787 Blood
0.746
4.1
27885
1270.3
322
57163.8
52
103116.2
0.970
title: GSM3304432 Blood_PSC_08, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Primary sclerosing cholangitis", "sex": "male", "age": "61", "body_mass_index": "20.8"}
SRX4452788 Blood
0.761
4.4
30409
1233.0
309
1433.2
68
89039.7
0.968
title: GSM3304433 Blood_PSC_09, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Primary sclerosing cholangitis", "sex": "male", "age": "30", "body_mass_index": "17.7"}
SRX4452789 Blood
0.745
3.9
24444
1388.5
199
92797.2
30
109656.4
0.960
title: GSM3304434 Blood_PSC_10, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Primary sclerosing cholangitis", "sex": "male", "age": "45", "body_mass_index": "37"}
SRX4452790 Blood
0.749
4.3
31138
1202.9
658
1175.9
168
69476.0
0.970
title: GSM3304435 Blood_WD_Hep_01, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "18", "body_mass_index": "28.1"}
SRX4452791 Blood
0.733
3.8
26433
1315.1
357
1193.4
58
106805.1
0.972
title: GSM3304436 Blood_WD_Hep_02, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "60", "body_mass_index": "25.7"}
SRX4452792 Blood
0.735
4.5
31555
1213.3
548
1336.8
95
76818.2
0.973
title: GSM3304437 Blood_WD_Hep_03, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "30", "body_mass_index": "24.4"}
SRX4452793 Blood
0.742
4.2
29434
1224.6
592
1332.2
137
78105.3
0.970
title: GSM3304438 Blood_WD_Hep_04, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "19", "body_mass_index": "27.2"}
SRX4452794 Blood
0.739
4.2
31277
1218.4
590
1190.6
75
83454.4
0.973
title: GSM3304439 Blood_WD_Hep_05, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "30", "body_mass_index": "25.2"}
SRX4452795 Blood
0.748
4.2
32412
1225.8
325
1472.3
89
86135.5
0.971
title: GSM3304440 Blood_WD_Hep_06, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "29", "body_mass_index": "29"}
SRX4452796 Blood
0.741
4.8
32600
1184.5
1079
1215.8
204
56961.9
0.973
title: GSM3304441 Blood_WD_Hep_07, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "23", "body_mass_index": "26"}
SRX4452797 Blood
0.739
4.7
31052
1195.0
1052
1271.7
76
76552.9
0.963
title: GSM3304442 Blood_WD_Hep_08, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "31", "body_mass_index": "29.5"}
SRX4452798 Blood
0.751
4.7
32956
1190.2
601
1250.5
182
59303.9
0.967
title: GSM3304443 Blood_WD_Hep_09, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "30", "body_mass_index": "27.2"}
SRX4452799 Blood
0.739
3.9
28205
1269.2
366
1157.4
58
108514.4
0.969
title: GSM3304444 Blood_WD_Hep_10, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "24", "body_mass_index": "21.4"}
SRX4452800 Blood
0.751
3.6
26370
1299.7
227
1263.4
88
99738.2
0.969
title: GSM3304445 Blood_WD_Hep_11, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "45", "body_mass_index": "33.1"}
SRX4452801 Blood
0.744
4.1
28997
1270.1
360
1185.9
66
88472.7
0.969
title: GSM3304446 Blood_WD_Hep_12, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "38", "body_mass_index": "28.6"}
SRX4452802 Blood
0.729
4.6
29242
1237.6
973
1368.2
37
87362.7
0.968
title: GSM3304447 Blood_WD_Hep_13, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "56", "body_mass_index": "20.4"}
SRX4452803 Blood
0.751
4.4
29549
1248.8
543
1192.2
153
69997.5
0.969
title: GSM3304448 Blood_WD_Hep_14, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "20", "body_mass_index": "22.1"}
SRX4452804 Blood
0.752
4.4
29423
1234.8
667
1230.2
112
75961.5
0.970
title: GSM3304449 Blood_WD_Hep_15, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "32", "body_mass_index": "22.9"}
SRX4452805 Blood
0.734
3.9
24234
1392.2
218
1761.3
32
105138.8
0.963
title: GSM3304450 Blood_WD_Hep_16, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "44", "body_mass_index": "19.7"}
SRX4452806 Blood
0.738
4.2
28839
1249.1
365
1471.1
66
104448.4
0.973
title: GSM3304451 Blood_WD_Hep_17, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "46", "body_mass_index": "25.7"}
SRX4452807 Blood
0.743
4.4
30273
1217.0
445
1382.7
67
101213.2
0.973
title: GSM3304452 Blood_WD_Hep_18, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "43", "body_mass_index": "32.6"}
SRX4452808 Blood
0.740
4.4
30707
1223.8
399
1452.6
54
112773.4
0.974
title: GSM3304453 Blood_WD_Hep_19, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "43", "body_mass_index": "20.1"}
SRX4452809 Blood
0.741
4.4
30114
1218.3
538
1236.9
113
81700.4
0.973
title: GSM3304454 Blood_WD_Hep_20, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "36", "body_mass_index": "22"}
SRX4452810 Blood
0.713
3.4
23089
1339.1
99
1312.9
44
330581.9
0.987
title: GSM3304455 Blood_WD_Hep_21, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "32", "body_mass_index": "N/A"}
SRX4452811 Blood
0.710
3.4
22941
1358.8
101
1210.9
16
284378.2
0.987
title: GSM3304456 Blood_WD_Hep_22, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "23", "body_mass_index": "N/A"}
SRX4452812 Blood
0.734
3.5
24255
1296.6
152
1117.4
33
201256.2
0.988
title: GSM3304457 Blood_WD_Hep_23, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "female", "age": "23", "body_mass_index": "N/A"}
SRX4452813 Blood
0.727
3.7
24284
1308.7
165
1495.7
23
171126.1
0.988
title: GSM3304458 Blood_WD_Hep_24, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "43", "body_mass_index": "N/A"}
SRX4452814 Blood
0.723
3.3
22793
1390.1
78
1245.5
25
203313.8
0.988
title: GSM3304459 Blood_WD_Hep_25, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease hepatic", "sex": "male", "age": "22", "body_mass_index": "N/A"}
SRX4452815 Blood
0.743
4.5
31332
1210.4
731
1305.5
80
80855.2
0.975
title: GSM3304460 Blood_WD_Neu_01, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "54", "body_mass_index": "20.2"}
SRX4452816 Blood
0.747
4.4
31659
1196.0
629
1247.1
91
90331.9
0.974
title: GSM3304461 Blood_WD_Neu_02, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "25", "body_mass_index": "31"}
SRX4452817 Blood
0.741
4.5
32807
1198.7
469
1318.1
75
87464.8
0.974
title: GSM3304462 Blood_WD_Neu_03, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "28", "body_mass_index": "19"}
SRX4452818 Blood
0.747
4.3
31122
1199.9
541
1164.0
119
79957.7
0.971
title: GSM3304463 Blood_WD_Neu_04, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "46", "body_mass_index": "23.2"}
SRX4452819 Blood
0.745
4.2
30071
1219.7
564
1134.9
129
73869.0
0.968
title: GSM3304464 Blood_WD_Neu_05, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "29", "body_mass_index": "23.5"}
SRX4452820 Blood
0.735
4.0
27402
1272.1
357
1363.7
62
102068.9
0.966
title: GSM3304465 Blood_WD_Neu_06, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "42", "body_mass_index": "30.7"}
SRX4452821 Blood
0.739
4.5
30646
1206.0
760
1221.8
115
69183.1
0.970
title: GSM3304466 Blood_WD_Neu_07, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "49", "body_mass_index": "22.7"}
SRX4452822 Blood
0.747
3.8
27670
1287.6
237
1454.0
67
103898.4
0.970
title: GSM3304467 Blood_WD_Neu_08, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "58", "body_mass_index": "25.3"}
SRX4452823 Blood
0.743
4.4
29340
1247.0
408
1329.6
116
87810.8
0.968
title: GSM3304468 Blood_WD_Neu_09, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "34", "body_mass_index": "28.3"}
SRX4452824 Blood
0.742
4.1
28096
1274.1
354
1262.6
50
121110.0
0.967
title: GSM3304469 Blood_WD_Neu_10, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "27", "body_mass_index": "18.2"}
SRX4452825 Blood
0.744
4.5
31396
1232.7
723
1243.9
115
70742.6
0.968
title: GSM3304470 Blood_WD_Neu_11, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "44", "body_mass_index": "26.4"}
SRX4452826 Blood
0.752
4.0
27404
1298.6
264
1659.3
53
98315.9
0.969
title: GSM3304471 Blood_WD_Neu_12, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "24", "body_mass_index": "18.9"}
SRX4452827 Blood
0.730
4.2
25726
1363.9
451
1370.6
53
100386.0
0.962
title: GSM3304472 Blood_WD_Neu_13, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "46", "body_mass_index": "24.5"}
SRX4452828 Blood
0.736
4.1
25541
1358.2
260
1225.8
31
122455.3
0.965
title: GSM3304473 Blood_WD_Neu_14, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "36", "body_mass_index": "24.7"}
SRX4452829 Blood
0.739
4.3
27282
1314.4
433
1235.3
95
89891.1
0.965
title: GSM3304474 Blood_WD_Neu_15, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "33", "body_mass_index": "25.8"}
SRX4452830 Blood
0.742
4.1
26337
1322.9
281
1437.7
73
87910.3
0.962
title: GSM3304475 Blood_WD_Neu_16, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "44", "body_mass_index": "25.7"}
SRX4452831 Blood
0.738
4.2
26825
1319.7
361
1246.6
87
115615.3
0.965
title: GSM3304476 Blood_WD_Neu_17, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "32", "body_mass_index": "30.2"}
SRX4452832 Blood
0.729
4.3
30427
1230.6
444
1522.9
65
89922.3
0.974
title: GSM3304477 Blood_WD_Neu_18, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "52", "body_mass_index": "22.7"}
SRX4452833 Blood
0.739
4.2
29469
1212.7
601
1158.0
72
95704.6
0.974
title: GSM3304478 Blood_WD_Neu_19, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "23", "body_mass_index": "24.3"}
SRX4452834 Blood
0.734
4.0
28166
1246.3
331
1371.7
61
101015.0
0.974
title: GSM3304479 Blood_WD_Neu_20, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "21", "body_mass_index": "28.7"}
SRX4452835 Blood
0.719
3.7
26459
1267.4
183
1243.6
66
172186.5
0.988
title: GSM3304480 Blood_WD_Neu_21, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "24", "body_mass_index": "N/A"}
SRX4452836 Blood
0.710
3.5
23649
1364.6
126
1676.4
16
223641.6
0.988
title: GSM3304481 Blood_WD_Neu_22, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "35", "body_mass_index": "N/A"}
SRX4452837 Blood
0.723
3.4
23500
1355.3
90
1105.7
63
192341.9
0.987
title: GSM3304482 Blood_WD_Neu_23, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "female", "age": "29", "body_mass_index": "N/A"}
SRX4452838 Blood
0.720
3.5
24767
1321.9
120
1609.6
33
192108.2
0.986
title: GSM3304483 Blood_WD_Neu_24, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "23", "body_mass_index": "N/A"}
SRX4452839 Blood
0.723
3.7
27207
1277.1
146
1557.4
48
132802.8
0.988
title: GSM3304484 Blood_WD_Neu_25, Homo sapiens, Bisulfite-Seq; {"source_name": "whole blood", "circumstances": "blood draw", "diagnosis": "Wilson disease neurologic", "sex": "male", "age": "31", "body_mass_index": "N/A"}
Methods
All analysis was done using a bisulfite sequnecing data analysis
pipeline DNMTools
developed in the Smith lab at USC.
Mapping reads from bisulfite sequencing :
Bisulfite treated reads are mapped to the genomes with the
abismal
Estimating methylation levels :
After reads are mapped and filtered, the
dnmtools counts command is used to obtain read
coverage and estimate methylation levels at individual cytosine
sites. We count the number of methylated reads (those containing a
C) and the number of unmethylated reads (those containing a T) at
each nucleotide in a mapped read that corresponds to a cytosine in
the reference genome. The methylation level of that cytosine is
estimated as the ratio of methylated to total reads covering that
cytosine. For cytosines in the symmetric CpG sequence context,
reads from the both strands are collapsed to give a single
estimate. Very rarely do the levels differ between strands
(typically only if there has been a substitution, as in a somatic
mutation), and this approach gives a better estimate.
Bisulfite conversion rate :
The bisulfite conversion rate for an experiment is estimated with
the dnmtools bsrate command, which computes the
fraction of successfully converted nucleotides in reads (those
read out as Ts) among all nucleotides in the reads mapped that map
over cytosines in the reference genome. This is done either using
a spike-in (e.g., lambda), the mitochondrial DNA, or the nuclear
genome. In the latter case, only non-CpG sites are used. While
this latter approach can be impacted by non-CpG cytosine
methylation, in practice it never amounts to much.
Identifying hypomethylated regions (HMRs) :
In most mammalian cells, the majority of the genome has high
methylation, and regions of low methylation are typically the
interesting features. (This seems to be true for essentially all
healthy differentiated cell types, but not cells of very early
embryogenesis, various germ cells and precursors, and placental
lineage cells.) These are valleys of low methylation are called
hypomethylated regions (HMR) for historical reasons. To identify
the HMRs, we use the dnmtools hmr command, which uses
a statistical model that accounts for both the methylation level
fluctations and the varying amounts of data available at each CpG
site.
Partially methylated domains :
Partially methylated domains are large genomic regions showing
partial methylation observed in immortalized cell lines and
cancerous cells. The pmd program is used to identify
PMDs.
Allele-specific methylation :
Allele-Specific methylated regions refers to regions where the
parental allele is differentially methylated compared to the
maternal allele. The program allelic is used to
compute allele-specific methylation score can be computed for each
CpG site by testing the linkage between methylation status of
adjacent reads, and the program amrfinder is used to
identify regions with allele-specific methylation.
For more detailed description of the methods of each step, please
refer to
the DNMTools
documentation .
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