Chromosome miRNA Start End Methylation Fold Change P-value Target Gene chr2 hsa-mir-7845 208031124 208031222 Hypomethlation -1.17746 0.000205 KLF7 chr2 hsa-mir-5001 233415184 233415283 Hypomethlation -1.10555 0.000806 EIF4E2;TIGD1 chr14 hsa-mir-376c 101506027 101506092 hypermethylation 1.42619 0.001340   chr3 hsa-mir-4444-2 75263627 75263700 hypermethylation 1.07197 0.001379   chr22 hsa-mir-3928 31556048 31556105 hypermethylation 1.14670 0.001707   chr19 hsa-mir-6795 15290094 15290161 Hypomethlation -1.00656 0.002333   chr22 hsa-mir-3653 29729147 29729256 hypermethylation 1.01139 0.002345   chr19 hsa-mir-520b 54204481 54204541 Hypomethlation -1.04360 0.002389   chr17 hsa-mir-33b 17717150 17717245 hypermethylation 1.01560 0.002862   chr19 hsa-mir-639 14640355 14640452 Hypomethlation -1.11001 0.003032 TECR;MIR639 chr9 hsa-mir-4674 139440625 139440711 Hypomethlation -1.14622 0.003294 NOTCH1 chr15 hsa-mir-3175 93447629 93447705 Hypomethlation -1.11911 0.003765 CHD2 chr14 hsa-mir-4710 105144031 105144086 Hypomethlation -1.12202 0.003959   chr8 hsa-mir-124-2 65291706 65291814 Hypomethlation -1.13882 0.004364   chr6 hsa-mir-6891 31323001 31323093 Hypomethlation -1.10710 0.004376   chr5 hsa-mir-143 148808481 148808586 hypermethylation 1.05776 0.005115   chr11 hsa-mir-130a 57408671 57408759 hypermethylation 1.02682 0.005571   chr11 hsa-mir-34c 111384164 111384240 Hypomethlation -1.14561 0.006109   chr11 hsa-mir-139 72326107 72326174 Hypomethlation -1.01062 0.008066   chr16 hsa-mir-1225 2140196 2140285 Hypomethlation -1.00302 0.008162   chr1 hsa-mir-760 94312388 94312467 hypermethylation 1.52577 0.008974   chr17 hsa-mir-142 56408593 56408679 hypomethylation -1.1211 0.009029   chr19 hsa-mir-638 10829080 10829179 hypermethylation 1.23848 0.009762 MIR638;DNM2 chr14 hsa-mir-496 101526910 101527011 hypomethylation -1.01214 0.009849   chr11 hsa-mir-1908 61582633 61582712 hypomethylation -1.08932 0.010624 MIR1908;FADS1 chr3 hsa-mir-425 49057581 49057667 hypermethylation 1.12229 0.010864 NDUFAF3;DALRD3; MIR425 chr13 hsa-mir-320d-1 41301964 41302011 hypermethylation 1.05393 0.011027   chr19 hsa-mir-523 54201639 54201725 hypomethylation -1.01830 0.011236   chr6 hsa-mir-6891 31323001 31323093 hypomethylation -1.34121 0.011631   chr19 hsa-mir-498 54177451 54177574 hypomethylation -1.01044 0.011972   chr20 hsa-mir-124-3 61809852 61809938 hypomethylation -1.12224 0.012418   chr10 hsa-mir-2110 115933864 115933938 hypomethylation -1.09673 0.012533   chr9 hsa-mir-6853 35732919 35732992 hypomethylation -1.05786 0.012640 CREB3;TLN1 chr3 hsa-mir-944 189547711 189547798 hypermethylation 1.02836 0.012847   chr11 hsa-mir-192 64658609 64658718 hypermethylation 1.00819 0.013255   chr1 hsa-mir-6742 228584749 228584810 hypermethylation 1.01184 0.013631   chr19 hsa-mir-4321 2250638 2250717 hypermethylation 1.06948 0.013643   chr8 hsa-mir-4664 144815253 144815323 hypermethylation 1.04538 0.014353   chr17 hsa-mir-3184 28444104 28444178 hypermethylation 1.44860 0.014434 MIR423;CCDC55 chr17 hsa-mir-423 28444097 28444190 hypermethylation 1.44860 0.014434 MIR423;CCDC55 chr5 hsa-mir-340 179442303 179442397 hypermethylation 1.01906 0.014508   chr8 hsa-mir-596 1765397 1765473 hypomethylation -1.19681 0.014675 MIR596 chr6 hsa-mir-6834 33258022 33258102 hypermethylation 1.07284 0.015375   chr2 hsa-mir-375 219866367 219866430 hypomethylation -1.56597 0.015549   chr19 hsa-mir-181c 13985513 13985622 hypermethylation 1.00944 0.015609   chr19 hsa-mir-181d 13985689 13985825 hypermethylation 1.00944 0.015609   chr4 hsa-mir-5091 13629489 13629581 hypermethylation 1.35117 0.016711 BOD1L chr20 hsa-mir-647 62573984 62574079 hypermethylation 1.01182 0.017086   chr1 hsa-mir-6733 43637323 43637383 hypomethylation -1.04073 0.017516 WDR65;EBNA1BP2 chr19 hsa-mir-330 46142252 46142345 hypomethylation -1.11000 0.018314 MIR330;EML2 chr8 hsa-mir-6876 25202918 25202990 hypermethylation 1.26651 0.018319   chr19 hsa-mir-4746 4445975 4446045 hypomethylation -1.00382 0.018569   chr2 hsa-mir-375 219866367 219866430 hypomethylation -1.38810 0.019266   chr19 hsa-mir-638 10829080 10829179 hypomethylation -1.09026 0.020249 DNM2 chr21 hsa-mir-155 26946292 26946356 hypomethylation -1.67121 0.020383   chr3 hsa-mir-15b 160122376 160122473 hypermethylation 1.07586 0.020474   chr3 hsa-mir-16-2 160122533 160122613 hypermethylation 1.07586 0.020474   chr19 hsa-mir-642a 46178186 46178282 hypermethylation 1.00701 0.020574   chr19 hsa-mir-642b 46178190 46178266 hypermethylation 1.00701 0.020574   chr22 hsa-mir-658 38240279 38240378 hypomethylation -1.16552 0.020627 ANKRD54;MIR658 chr3 hsa-let-7g 52302294 52302377 hypomethylation -1.15178 0.021046   chr15 hsa-mir-4515 83736087 83736167 hypomethylation -1.05581 0.021243 BTBD1 chr17 hsa-mir-4523 27717680 27717748 hypomethylation -1.14820 0.021784   chr7 hsa-mir-6840 99954274 99954344 hypermethylation 1.01168 0.022112   chr17 hsa-mir-10a 46657200 46657309 hypermethylation 1.14698 0.022855   chr20 hsa-mir-124-3 61809852 61809938 hypomethylation -1.10597 0.023198   chr17 hsa-mir-4523 27717680 27717748 hypermethylation 1.32887 0.023291   chr2 hsa-mir-3679 134884696 134884763 hypomethylation -1.02140 0.023375   chr1 hsa-mir-6733 43637323 43637383 hypomethylation -1.47410 0.023379 WDR65;EBNA1BP2 chr3 hsa-mir-4792 24562853 24562926 hypomethylation -1.11756 0.023586   chr17 hsa-mir-1288 16185328 16185402 hypermethylation 1.03806 0.023703   chr2 hsa-mir-4444-1 178077454 178077527 hypermethylation 1.10018 0.023789 HNRNPA3 chr17 hsa-mir-378j 35974976 35975084 hypomethylation -1.00674 0.024333   chr2 hsa-mir-1471 232756952 232757008 hypomethylation -1.00916 0.024522   chr17 hsa-mir-632 30677128 30677221 hypomethylation -1.17464 0.025691 ZNF207;MIR632 chr11 hsa-mir-1304 93466840 93466930 hypermethylation 1.11806 0.026275   chr15 hsa-mir-3175 93447629 93447705 hypomethylation -1.14724 0.026841 CHD2 chr20 hsa-mir-663a 26188822 26188914 hypomethylation -1.16412 0.026892 MIR663 chr9 hsa-mir-4672 130631694 130631774 hypomethylation -1.00712 0.027149   chr3 hsa-mir-885 10436173 10436246 hypomethylation -1.00941 0.027299   chr7 hsa-mir-183 129414745 129414854 hypermethylation 1.01084 0.027378   chr7 hsa-mir-96 129414532 129414609 hypermethylation 1.01084 0.027380   chr12 hsa-mir-141 7073260 7073354 hypermethylation 1.01399 0.027805   chr7 hsa-mir-590 73605528 73605624 hypomethylation -1.01026 0.028022   chr12 hsa-mir-1178 120151439 120151529 hypermethylation 1.01277 0.028608   chr4 hsa-mir-1973 117220881 117220924 hypermethylation 1.08332 0.028757   chr2 hsa-mir-375 219866367 219866430 hypomethylation -1.29192 0.029281   chr10 hsa-mir-2110 115933864 115933938 hypomethylation -1.09997 0.029535 MIR2110;C10orf118 chr10 hsa-mir-1296 65132717 65132808 hypermethylation 1.01367 0.029866   chr19 hsa-mir-23a 13947401 13947473 hypermethylation 1.06274 0.029990 MIR27A;MIR24-2 chr19 hsa-mir-24-2 13947101 13947173 hypermethylation 1.06274 0.029990   chr19 hsa-mir-27a 13947254 13947331 hypermethylation 1.06274 0.029990 MIR27A;MIR24-2 chr17 hsa-mir-152 46114527 46114613 hypomethylation -1.30883 0.030070 MIR152;COPZ2 chr17 hsa-mir-6516 75085499 75085579 hypermethylation 1.14486 0.030396 SCARNA16;  C17orf86 chr8 hsa-mir-320a 22102475 22102556 hypermethylation 1.08542 0.030987 POLR3D;MIR320A chr1 hsa-mir-320b-2 224444706 224444843 hypomethylation -1.00847 0.031140   chr1 hsa-mir-5087 147806603 147806678 hypomethylation -1.47707 0.031743   chr17 hsa-mir-4521 8090263 8090322 hypomethylation -1.10388 0.032254   chr14 hsa-mir-496 101526910 101527011 hypomethylation -1.01232 0.033237   chr1 hsa-mir-320b-1 117214371 117214449 hypermethylation 1.01642 0.033722   chr2 hsa-mir-933 176032361 176032437 hypermethylation 1.15198 0.033760 ATF2;MIR933 chr12 hsa-mir-7107 121882076 121882155 hypermethylation 1.01076 0.033806 KDM2B chr14 hsa-mir-6717 21491473 21491545 hypermethylation 1.03920 0.033889   chr7 hsa-mir-4648 2566708 2566779 hypermethylation 1.00823 0.034164   chr10 hsa-mir-938 29891193 29891275 hypomethylation -1.00845 0.034456   chr6 hsa-mir-6832 31601564 31601635 hypermethylation 1.00795 0.034535   chr15 hsa-mir-627 42491768 42491864 hypomethylation -1.01772 0.035449   chr3 hsa-mir-128-2 35785968 35786051 hypermethylation 1.01399 0.035564   chr3 hsa-mir-4444-2 75263627 75263700 hypermethylation 1.06916 0.035786   chr14 hsa-mir-300 101507700 101507782 hypermethylation 1.40643 0.036924   chr6 hsa-mir-6891 31323001 31323093 hypomethylation -1.13122 0.037499   chr17 hsa-mir-142 56408593 56408679 hypomethylation -1.10981 0.038468   chr14 hsa-mir-409 101531637 101531715 hypomethylation -1.01538 0.038623   chr14 hsa-mir-412 101531784 101531874 hypomethylation -1.01538 0.038623   chr15 hsa-mir-628 55665138 55665232 hypermethylation 1.06044 0.038658   chr13 hsa-mir-8073 110993305 110993376 hypomethylation -1.12176 0.039730   chr4 hsa-mir-572 11370451 11370545 hypermethylation 1.13340 0.040330   chr22 hsa-mir-3928 31556048 31556105 hypermethylation 1.20598 0.040468   chr14 hsa-mir-4505 74225450 74225522 hypomethylation -1.10764 0.040469   chr17 hsa-mir-365b 29902430 29902540 hypomethylation -1.00811 0.040829   chr17 hsa-mir-4725 29902288 29902377 hypomethylation -1.00811 0.040829   chr19 hsa-mir-4754 58898137 58898225 hypomethylation -1.12062 0.040839 RPS5 chr5 hsa-mir-1229 179225278 179225346 hypomethylation -1.00370 0.041022   chr15 hsa-mir-7706 85923827 85923893 hypomethylation -1.10880 0.041546 AKAP13 chr11 hsa-mir-4492 118781417 118781496 hypomethylation -1.13724 0.042569 BCL9L chr18 hsa-mir-4741 20513312 20513401 hypomethylation -1.13235 0.042592 RBBP8 chr13 hsa-mir-19a 92003145 92003226 hypermethylation 1.03689 0.043500   chr13 hsa-mir-19b-1 92003446 92003532 hypermethylation 1.03689 0.043500   chr13 hsa-mir-20a 92003319 92003389 hypermethylation 1.03689 0.043500   chr13 hsa-mir-92a-1 92003568 92003645 hypermethylation 1.03689 0.043500   chr12 hsa-mir-7107 121882076 121882155 hypomethylation -1.00568 0.044221 KDM2B chr8 hsa-mir-661 145019359 145019447 hypermethylation 1.01970 0.044401   chr14 hsa-mir-4308 55344831 55344911 hypermethylation 1.00911 0.044475   chr12 hsa-mir-1251 97885687 97885756 hypermethylation 1.02643 0.045113   chr5 hsa-mir-4638 180649566 180649633 hypermethylation 1.03734 0.045950 TRIM41 chr11 hsa-mir-4687 3877292 3877371 hypomethylation -1.06416 0.046474 STIM1 chr19 hsa-mir-1909 1816158 1816237 hypermethylation 1.01084 0.046474   chr10 hsa-mir-1307 105154010 105154158 hypermethylation 1.01492 0.046703   chr19 hsa-mir-769 46522190 46522307 hypermethylation 1.02118 0.046976   chr3 hsa-mir-6828 170140891 170140950 hypomethylation -1.00978 0.047242   chr7 hsa-mir-339 1062569 1062662 hypermethylation 1.02186 0.047576   chr1 hsa-mir-181a-1 198828173 198828282 hypermethylation 1.02246 0.048357   chr1 hsa-mir-181b-1 198828002 198828111 hypermethylation 1.02246 0.048356   chr14 hsa-mir-369 101531935 101532004 hypomethylation -1.00698 0.048589   chr14 hsa-mir-409 101531637 101531715 hypomethylation -1.00698 0.048589   chr14 hsa-mir-412 101531784 101531874 hypomethylation -1.00698 0.048589   chr7 hsa-mir-196b 27209099 27209182 hypomethylation -1.09179 0.048613 MIR196B chr11 hsa-mir-675 2017989 2018061 hypomethylation -1.01792 0.048989   chr19 hsa-mir-638 10829080 10829179 hypomethylation -1.15170 0.049180 DNM2;MIR638 chr11 hsa-mir-34c 111384164 111384240 hypomethylation -1.04702 0.049253   chr2 hsa-mir-5703 228336848 228336903 hypomethylation -1.11947 0.049776 AGFG1 chr8 hsa-mir-6850 146017316 146017376 hypomethylation -1.25334 0.050049 RPL8 chr6 hsa-mir-6891 31323001 31323093 hypomethylation -1.16699 0.050185   chr2 hsa-mir-5001 233415184 233415283 hypomethylation -1.08397 0.050224 EIF4E2;TIGD1 chr11 hsa-mir-194-2 64658827 64658911 hypomethylation -1.00694 0.051008   chr17 hsa-mir-33b 17717150 17717245 hypermethylation 1.01486 0.051177   chr17 hsa-mir-6777 17716794 17716859 hypermethylation 1.01486 0.051177   chr22 hsa-mir-3653 29729147 29729256 hypermethylation 1.01870 0.051352   chr14 hsa-mir-127 101349316 101349412 hypomethylation -1.01120 0.051369   chr19 hsa-mir-519a-2 54265598 54265684 hypermethylation 1.02831 0.051921   chr14 hsa-mir-369 101531935 101532004 hypomethylation -1.00538 0.052194   chr14 hsa-mir-409 101531637 101531715 hypomethylation -1.00538 0.052194   chr14 hsa-mir-412 101531784 101531874 hypomethylation -1.00538 0.052194   chr19 hsa-mir-638 10829080 10829179 hypomethylation -1.07948 0.052329 DNM2;MIR638 chr7 hsa-mir-550a-2 32772593 32772689 hypomethylation -1.03930 0.052335   chr7 hsa-mir-550b-2 32772593 32772689 hypomethylation -1.03930 0.052335   chr14 hsa-mir-1247 102026624 102026759 hypomethylation -1.09325 0.052954 DIO3 chr8 hsa-mir-1208 129162362 129162434 hypermethylation 1.02168 0.053031   chr22 hsa-mir-1286 20236657 20236734 hypermethylation 1.01313 0.053109   chr1 hsa-mir-4259 159869769 159869869 hypomethylation -1.06762 0.053249   chr1 hsa-mir-200b 1102484 1102578 hypermethylation 1.01675 0.053309 MIR200B;MIR200A chr9 hsa-mir-204 73424891 73425000 hypermethylation 1.00784 0.053460   chr16 hsa-mir-662 820183 820277 hypomethylation -1.01052 0.053469   chr4 hsa-mir-572 11370451 11370545 hypermethylation 1.08956 0.054065   chr2 hsa-mir-933 176032361 176032437 hypermethylation 1.28796 0.054611 ATF2;MIR933 chr16 hsa-mir-762 30905224 30905306 hypomethylation -1.08783 0.054681 BCL7C;MIR762

Table 2: A list of miRNA genes with differential methylated regions in the CFS/ME patients in comparison to controls.