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Table 1 The 100 CpG sites with the lowest combined rank scores

From: Genome-wide identification of methylated CpG sites in nongenital cutaneous warts

CpG Chromosome Gene Methylation region CpG Island Mean β value (NS) Mean β value (W) Mean β value diff (W-NS) mean.quot. (log2) P-value False discovery rate Combined rank score Methylation pattern
cg09671951 10 C10orf26 Body   0.1129 0.5848 0.4719 2.2753 6.82E-16 5.09E-11 48 Hypermethylation
cg27071672 8 FAM83H- AS1 Body S_Shelf 0.1290 0.5765 0.4475 2.0772 1.74E-14 1.99E-10 102 Hypermethylation
cg07385604 1 ZNF644 TSS1500 S_Shore 0.1281 0.5720 0.4440 2.0756 9.33E-16 5.09E-11 110 Hypermethylation
cg12432168 10 LINC00702 Body   0.1558 0.6389 0.4832 1.9690 6.83E-15 1.31E-10 151 Hypermethylation
cg06305962 7 GSAP Body   0.1249 0.5457 0.4208 2.0421 1.49E-14 1.91E-10 183 Hypermethylation
cg00071017 2     0.6112 0.1537 −0.4575 −1.9241 7.83E-16 5.09E-11 186 Hypomethylation
cg16530881 17     0.1080 0.5208 0.4127 2.1688 1.99E-13 7.07E-10 236 Hypermethylation
cg08246644 17 STAT5A TSS1500;5’UTR;TS
S200
N_Shore 0.1009 0.5098 0.4089 2.2286 2.29E-15 7.97E-11 245 Hypermethylation
cg05171197 2 HDAC4 Body   0.1973 0.7523 0.5550 1.8785 1.65E-13 6.32E-10 247 Hypermethylation
cg16516970 8 NCALD 5’UTR   0.1567 0.6028 0.4461 1.8783 2.74E-14 2.4E-10 248 Hypermethylation
cg03432603 7 EXOC4 Body   0.6423 0.1335 −0.5088 −2.1842 2.14E-13 7.24E-10 249 Hypomethylation
cg01890417 1 ZNF644 TSS1500 S_Shore 0.1519 0.5773 0.4254 1.8592 2.75E-14 2.4E-10 274 Hypermethylation
cg00194325 2 TANC1 Body   0.1719 0.6446 0.4727 1.8473 5.54E-16 5.09E-11 290 Hypermethylation
cg25894955 9 ABCA1 Body   0.5371 0.1351 −0.4021 −1.9151 2.81E-14 2.4E-10 295 Hypomethylation
cg10560060 13 GJB2 5’UTR N_Shelf 0.6623 0.1799 −0.4824 − 1.8238 2.4E-13 7.66E-10 329 Hypomethylation
cg10144055 2     0.1350 0.5324 0.3974 1.9032 7.42E-15 1.34E-10 336 Hypermethylation
cg19342952 13 GJB2 5’UTR N_Shore 0.6449 0.1770 −0.4679 −1.8080 5.82E-14 3.81E-10 347 Hypomethylation
cg15612257 2    N_Shore 0.1547 0.5655 0.4108 1.8048 2.56E-15 7.97E-11 359 Hypermethylation
cg07863022 17 SEPT9; 5’UTR;Body;TSS15
00
  0.1681 0.6076 0.4395 1.7937 3.99E-15 9.85E-11 375 Hypermethylation
cg02745009 3 ARHGAP3 1 Body S_Shore 0.1718 0.6135 0.4417 1.7783 2.9E-13 8.24E-10 407 Hypermethylation
cg15782771 5     0.7396 0.2096 −0.5299 −1.7709 3.84E-14 3.03E-10 428 Hypomethylation
cg04272613 14 DAAM1 5’UTR   0.1508 0.5378 0.3869 1.7680 2.74E-15 7.97E-11 445 Hypermethylation
cg10017626 2    N_Shore 0.0988 0.4854 0.3866 2.1870 2.02E-13 7.07E-10 449 Hypermethylation
cg18248499 11 ROBO4 TSS1500   0.5057 0.1193 −0.3865 −1.9961 3.43E-13 9.24E-10 451 Hypomethylation
cg10841463 14     0.1646 0.5798 0.4153 1.7566 7.01E-17 1.69E-11 457 Hypermethylation
cg19497037 11     0.5188 0.1328 −0.3860 −1.8891 7.48E-13 1.37E-09 459 Hypomethylation
cg13800897 2     0.5754 0.1613 −0.4141 −1.7727 8.99E-13 1.55E-09 490 Hypomethylation
cg13632752 8     0.5831 0.1474 −0.4357 −1.9140 9.15E-13 1.56E-09 494 Hypomethylation
cg27277339 15 MYO5C Body   0.1561 0.5455 0.3894 1.7417 9.65E-14 4.88E-10 496 Hypermethylation
cg19158326 22 GRAMD4 Body   0.0980 0.4793 0.3813 2.1796 3.91E-15 9.85E-11 514 Hypermethylation
cg20400915 17 STAT5A TSS1500;5’UTR;TS
S200
N_Shore 0.0555 0.4492 0.3937 2.8086 1.02E-12 1.66E-09 519 Hypermethylation
cg20392201 1 FAM129A Body   0.1263 0.5848 0.4585 2.1258 1.04E-12 1.69E-09 521 Hypermethylation
cg21879102 12 CIT Body N_Shore 0.1946 0.6605 0.4659 1.7127 2.61E-13 7.91E-10 549 Hypermethylation
cg14384093 9 C9orf5 Body N_Shelf 0.1256 0.5097 0.3841 1.9381 1.25E-12 1.9E-09 557 Hypermethylation
cg18813270 2 HS1BP3-
IT1
TSS1500   0.6868 0.1911 −0.4957 −1.7929 1.3E-12 1.95E-09 564 Hypomethylation
cg19449565 2 HDAC4 Body   0.1691 0.6536 0.4845 1.8898 1.33E-12 1.96E-09 570 Hypermethylation
cg09187774 10     0.6165 0.1627 −0.4538 −1.8593 1.34E-12 1.98E-09 572 Hypomethylation
cg07980148 4    S_Shelf 0.6475 0.1624 −0.4852 −1.9317 1.36E-12 1.99E-09 573 Hypomethylation
cg03304533 11     0.6668 0.1977 −0.4690 −1.7040 3.09E-13 8.67E-10 576 Hypomethylation
cg08569613 17 STAT5A TSS1500;5’UTR;TS
S200
N_Shore 0.0692 0.4453 0.3761 2.5226 6.22E-15 1.25E-10 578 Hypermethylation
cg06848849 1 ARHGEF10
L
Body   0.1451 0.5204 0.3753 1.7737 2.84E-14 2.4E-10 591 Hypermethylation
cg17164954 6 ARID1B Body S_Shelf 0.1656 0.5604 0.3948 1.6997 6.39E-13 1.24E-09 591 Hypermethylation
cg13733684 15 ZNF106 TSS200;Body   0.1724 0.5807 0.4083 1.6954 1.72E-14 1.99E-10 603 Hypermethylation
cg05669832 2 PRKD3 TSS1500   0.2068 0.6911 0.4843 1.6934 2.72E-13 8.02E-10 611 Hypermethylation
cg06382539 12 BHLHE41 Body N_Shore 0.1759 0.5882 0.4123 1.6864 1.58E-12 2.14E-09 629 Hypermethylation
cg16303737 20     0.5411 0.1618 −0.3793 −1.6819 7.37E-13 1.36E-09 642 Hypomethylation
cg27335585 5 LOC101929
710
Body   0.7606 0.2298 −0.5308 − 1.6840 1.78E-12 2.31E-09 652 Hypomethylation
cg09185727 6     0.5467 0.1642 −0.3825 −1.6763 2.73E-13 8.02E-10 652 Hypomethylation
cg15350314 3 LOC101928
992
Body   0.1552 0.5574 0.4021 1.7797 1.85E-12 2.36E-09 658 Hypermethylation
cg11508674 14 FOXN3 Body   0.1648 0.6344 0.4696 1.8820 2.02E-12 2.49E-09 683 Hypermethylation
cg06610988 18 SETBP1 5’UTR S_Shore 0.1684 0.5546 0.3862 1.6622 3.94E-14 3.06E-10 684 Hypermethylation
cg18492160 15     0.5276 0.1311 −0.3965 −1.9299 2.03E-12 2.49E-09 690 Hypomethylation
cg02921273 20     0.0980 0.4645 0.3664 2.1349 3.95E-14 3.06E-10 699 Hypermethylation
cg14167109 11 MAML2 Body   0.1594 0.5381 0.3787 1.6939 2.13E-12 2.55E-09 703 Hypermethylation
cg06373653 12 CD163L1 Body   0.4932 0.1277 −0.3656 −1.8699 2.3E-13 7.47E-10 709 Hypomethylation
cg09403144 18 SETBP1 Body   0.1549 0.5202 0.3653 1.6847 3.68E-14 2.96E-10 714 Hypermethylation
cg06746371 6 DCBLD1 Body   0.7344 0.2249 −0.5095 −1.6641 2.31E-12 2.68E-09 727 Hypomethylation
cg14002969 20 PTPRA 5’UTR   0.4985 0.1342 −0.3644 −1.8187 5.04E-13 1.11E-09 727 Hypomethylation
cg07076915 16 PKD1 Body N_Shelf 0.2112 0.6851 0.4739 1.6517 2.48E-14 2.32E-10 728 Hypermethylation
cg27341747 6     0.2010 0.6524 0.4514 1.6503 5.21E-14 3.61E-10 732 Hypermethylation
cg20964957 4     0.5612 0.1185 −0.4428 −2.1527 2.39E-12 2.74E-09 736 Hypomethylation
cg19917507 18 ALPK2 Body   0.5863 0.1813 −0.4050 −1.6401 4.78E-13 1.08E-09 757 Hypomethylation
cg00925616 1    Island 0.0781 0.5172 0.4392 2.5818 2.61E-12 2.89E-09 762 Hypermethylation
cg13515269 12 BHLHE41 3’UTR N_Shore 0.2078 0.6886 0.4809 1.6818 2.71E-12 2.96E-09 772 Hypermethylation
cg18638180 21 C21orf70 Body S_Shore 0.1734 0.6318 0.4584 1.8073 2.93E-12 3.13E-09 791 Hypermethylation
cg17967134 17 MPRIP Body   0.1283 0.4884 0.3601 1.8495 1.19E-12 1.83E-09 804 Hypermethylation
cg06373648 6 SYNGAP1 Body   0.1564 0.5160 0.3596 1.6604 4.57E-13 1.06E-09 818 Hypermethylation
cg14825152 1     0.1422 0.5010 0.3588 1.7475 4.83E-13 1.09E-09 828 Hypermethylation
cg08966889 6 TRAM2 Body N_Shore 0.1747 0.5588 0.3840 1.6224 1.16E-12 1.81E-09 828 Hypermethylation
cg09443467 5 TENM2 Body   0.5807 0.1623 −0.4185 −1.7779 3.44E-12 3.49E-09 833 Hypomethylation
cg17758398 18     0.6251 0.1850 −0.4401 −1.7035 3.48E-12 3.51E-09 836 Hypomethylation
cg01821452 12     0.2138 0.6779 0.4641 1.6198 1.44E-12 2.06E-09 840 Hypermethylation
cg19663114 3 MED12L Body   0.7670 0.2279 −0.5390 −1.7073 3.64E-12 3.6E-09 853 Hypomethylation
cg10624729 1 FAM73A Body   0.1847 0.5864 0.4017 1.6152 1.53E-13 6.05E-10 857 Hypermethylation
cg26586287 11     0.6087 0.1625 −0.4463 −1.8430 3.74E-12 3.67E-09 859 Hypomethylation
cg23983887 1 VPS13D Body   0.1546 0.5113 0.3567 1.6629 1.65E-12 2.21E-09 866 Hypermethylation
cg08921063 6 WASF1 5’UTR   0.4750 0.1185 −0.3565 −1.9164 2.02E-12 2.49E-09 871 Hypomethylation
cg14359656 17 SPAG9 Body   0.5856 0.1477 −0.4380 −1.9176 3.98E-12 3.81E-09 883 Hypomethylation
cg26754187 3     0.5241 0.1368 −0.3873 −1.8634 4E-12 3.81E-09 885 Hypomethylation
cg10126884 4     0.4827 0.1254 −0.3573 −1.8635 4.05E-12 3.85E-09 888 Hypomethylation
cg13355857 16     0.6967 0.1872 −0.5096 −1.8418 4.06E-12 3.85E-09 889 Hypomethylation
cg13568540 7 PKD1L1 Body   0.6599 0.1847 −0.4752 −1.7828 4.22E-12 3.95E-09 901 Hypomethylation
cg08611640 1 VPS13D Body;Body   0.1109 0.4654 0.3546 1.9757 7.7E-15 1.34E-10 912 Hypermethylation
cg25322618 2 RAPGEF4 TSS200;Body   0.2041 0.6388 0.4347 1.5994 1.22E-13 5.62E-10 913 Hypermethylation
cg16669099 6     0.1801 0.5652 0.3851 1.5971 3.77E-12 3.69E-09 919 Hypermethylation
cg19712663 6 SLC22A23 Body   0.1017 0.4711 0.3694 2.1069 4.47E-12 4.07E-09 927 Hypermethylation
cg13720639 14 SIPA1L1 Body   0.1299 0.4946 0.3646 1.8502 4.5E-12 4.08E-09 929 Hypermethylation
cg04394003 12 C12orf75 TSS1500 N_Shore 0.1172 0.4703 0.3531 1.9170 3.46E-12 3.51E-09 931 Hypermethylation
cg17356718 2 HDAC4 Body   0.1435 0.5270 0.3835 1.8066 4.51E-12 4.08E-09 931 Hypermethylation
cg26639076 2 RIF1 3’UTR   0.1710 0.5360 0.3650 1.5930 7.11E-14 4.2E-10 936 Hypermethylation
cg07969739 10 BTAF1 Body   0.5137 0.1346 −0.3791 −1.8564 4.74E-12 4.17E-09 958 Hypomethylation
cg26125625 3 SLC12A8 Body Island 0.1074 0.4587 0.3513 1.9968 2.24E-12 2.64E-09 965 Hypermethylation
cg18251218 1     0.0952 0.4461 0.3510 2.1169 1.17E-16 1.69E-11 967 Hypermethylation
cg23909079 10 GRID1 Body   0.6723 0.2146 −0.4577 −1.6031 4.92E-12 4.25E-09 977 Hypomethylation
cg24117274 1 RAP1GAP Body N_Shelf 0.1260 0.4766 0.3505 1.8387 7.37E-14 4.29E-10 979 Hypermethylation
cg09262171 16 ADCY9 Body   0.1896 0.5865 0.3970 1.5796 3.41E-14 2.78E-10 992 Hypermethylation
cg14600452 10     0.6088 0.1865 −0.4223 −1.6550 5.44E-12 4.53E-09 1014 Hypomethylation
cg24088496 11 MAML2 Body   0.1856 0.5727 0.3871 1.5747 1.73E-13 6.44E-10 1016 Hypermethylation
cg06968781 1 GMEB1 5’UTR   0.5323 0.1666 −0.3657 −1.6189 5.65E-12 4.63E-09 1030 Hypomethylation
cg03133881 1 MAST2 Body   0.5066 0.1589 −0.3477 −1.6128 5.41E-12 4.52E-09 1035 Hypomethylation