Table 1:
DMS found in genes or gene promoter regions (q value < 0.005 and differential methylation ≥ 10%)
| Chr | Position | Difference between TCE and control methylation | Refseq ID | Feature name | PcG | Other TF with PcG |
|---|---|---|---|---|---|---|
| chr1 | 52733087 | 19.80 | NM_133829 | Mfsd6 | None | None |
| chr1 | 72871428 | 10.11 | NM_008342 | Igfbp2 | None | None |
| chr1 | 84692366 | –12.74 | NM_152915 | Dner | Mtf2 | |
| chr1 | 87915123 | 12.38 | NM_027029 | Spata3 | Mtf2, Suz12, EZH2, Jarid2 | |
| chr1 | 87915176 | 10.91 | NM_027029 | Spata3 | Mtf2, Suz12, EZH2, Jarid2 | |
| chr1 | 88566769 | –11.67 | NM_010933 | Nppc | Suz12, EZH2, Jarid2 | |
| chr1 | 95079010 | 21.05 | NM_001310428 | Crocc2 | None | None |
| chr10 | 57695435 | 19.10 | NM_001081954 | Dux | Mtf2 | |
| chr10 | 59348501 | 38.10 | NM_019965 | Dnajb12 | None | Ebf1 |
| chr10 | 70622501 | 12.01 | NM_031397 | Bicc1 | Mtf2, Suz12, EZH2, Jarid2 | |
| chr10 | 80297554 | 26.59 | NM_001013758 | Lingo3 | Mtf2, Suz12, EZH2 | |
| chr10 | 80306503 | 13.08 | NM_001013758 | Lingo3 | Mtf2, Suz12, EZH2 | |
| chr10 | 114239413 | –17.84 | NM_146241 | POL2 | Mtf2, Suz12, EZH2, Jarid2 | |
| chr10 | 126954849 | 24.03 | NM_001098789 | Shmt2 | None | |
| chr10 | 126962175 | –15.64 | NM_028230 | Nxph4 | Mtf2, Suz12 | |
| chr10 | 127733967 | –12.19 | NM_031252 | Il23a | None | |
| chr11 | 8496658 | 22.56 | NM_001083587 | Tns3 | None | None |
| chr11 | 50416921 | –11.01 | NM_175643 | Adamts2 | Mtf2, Suz12, EZH2, Jarid2 | |
| chr11 | 53271010 | –23.32 | NM_027917 | Schroom1 | Mtf2, Suz12 | |
| chr11 | 61267631 | 27.93 | NM_009548 | Rnf112 | None | None |
| chr11 | 92958940 | –13.88 | NM_028296 | Car 10 | Mtf2, Suz12 | |
| chr11 | 95692072 | 29.58 | NM_025659 | Abi3 | Mtf2, Suz12, EZH2 | |
| chr11 | 103222902 | 10.07 | NM_001205236 | h3d20 | None | |
| chr11 | 113664146 | –20.41 | NM_172800 | Sdk2 | None | |
| chr11 | 117829957 | –13.33 | NM_007707 | Socs3 | None | |
| chr11 | 121691565 | 22.39 | NM_029049 | Ptchd3 | Mtf2, Suz12 | |
| chr12 | 25366541 | 16.22 | NM_001004455 | Cys1 | Mtf2, EZH2 | |
| chr12 | 28026694 | 18.76 | NM_009234 | Sox11 | Mtf2, Suz12, EZH2 | |
| chr12 | 51749480 | 14.75 | NM_008858 | Prdk1 | Mtf2, Jarid2 | |
| chr12 | 51749594 | 22.12 | NM_008858 | Prdk1 | Mtf2, Jarid2 | |
| chr12 | 77506059 | 13.22 | NM_008301 | Hspa2 | Mtf2, Jarid2, EZH2, Jarid2 | |
| chr12 | 81071379 | 17.08 | NM_001252562 | Rad51b | None | Ebf1 |
| chr12 | 81216463 | –18.69 | NM_007564 | Zfp36l1 | Mtf2 | |
| chr12 | 81794135 | 20.44 | NM_001177503 | Plekhd1 | Mtf2, Suz12 | |
| chr12 | 84828460 | 27.36 | NM_001267625 | Dpf3 | Mtf2, Jarid2, EZH2, Jarid2 | |
| chr12 | 84828462 | 32.76 | NM_001267625 | Dpf3 | Mtf2, Jarid2, EZH2,Suz12 | |
| chr12 | 85758595 | 20.16 | NM_025525 | Bbof1 | None | None |
| chr12 | 86630006 | –21.49 | NM_172414 | Zc2hc1c | None | None |
| chr12 | 111468610 | 28.44 | NM_012023 | Ppp2r5c | None | None |
| chr13 | 49168362 | –23.74 | NM_001290313 | Wnk2 | None | None |
| chr13 | 53560005 | –23.88 | NM_013601 | Msx2 | Mtf2 | |
| chr13 | 55097204 | –16.10 | NM_001206390 | Unca5 | None | None |
| chr13 | 69137738 | 17.13 | NM_153534 | Adcy2 | EZH2, Mtf2 | |
| chr13 | 104899736 | –10.66 | NM_029447 | N1n | None | None |
| chr13 | 110249606 | –21.25 | NM_011056 | Pde4d | None | None |
| chr14 | 55195182 | –22.04 | NM_010590 | Ajuba | None | None |
| chr14 | 64478548 | –26.58 | NM_028228 | Pinx1 | None | None |
| chr15 | 7763733 | –10.39 | NM_001301333 | Gdnf | Mtf2, Jarid2, EZH2, Suz12 | |
| chr15 | 39751326 | 26.27 | NM_172814 | Lrp12 | None | None |
| chr15 | 78548459 | –21.71 | NM_183141 | Elfn2 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr15 | 78873745 | –10.38 | NM_015738 | Galr3 | Suz12, EZH2 | |
| chr15 | 79920093 | 22.09 | NM_009303 | Syngr1 | None | None |
| chr15 | 91729910 | 11.19 | NM_198927 | Muc19 | None | None |
| chr15 | 101858889 | –20.17 | NM_010664 | Krt18 | Mtf2 | |
| chr15 | 22440834 | 24.56 | NM_023794 | Etv5 | None | None |
| chr16 | 65815534 | 17.40 | NM_028572 | Vg113 | None | ATOH1 |
| chr16 | 72682095 | 11.64 | NM_019413 | Robo1 | None | None |
| chr16 | 84989074 | 13.29 | NM_001198823 | App | None | None |
| chr17 | 11806358 | 26.52 | NM_016694 | Park2 | None | None |
| chr17 | 26204880 | –17.06 | NM_001162868 | Rab11fip3 | Mtf1 | |
| chr17 | 27787774 | 30.42 | NM_001286743 | Pascin1 | None | None |
| chr17 | 32326330 | 14.78 | NM_001033163 | Ephx3 | Mtf2 | |
| chr17 | 35033560 | 20.63 | NM_001286575 | Zbtb12 | None | None |
| chr17 | 47809520 | 26.89 | NM_198421 | Usp49 | None | None |
| chr17 | 80112667 | 10.22 | NM_009994 | Cyb1b1 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr17 | 86014548 | 20.07 | NM_198421 | SIX30S1 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr18 | 7170227 | –15.42 | NM_001081393 | Armc4 | None | None |
| chr18 | 11997673 | 11.79 | NM_001146287 | Cables1 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr18 | 37926514 | 26.30 | NM_033595 | Pcdhga12 | Suz12 | |
| chr18 | 46372273 | –16.68 | NM_178872 | Trim36 | Suz12, Mtf2 | |
| chr18 | 74603497 | –26.02 | NM_201600 | Myo5b | EZH2, Mtf2 | |
| chr18 | 75980831 | –36.51 | NM_145356 | Zbtb7c | Mtf2, Jarid2, EZH2, Suz12 | |
| chr19 | 5332047 | –28.01 | NM_139301 | Catsper1 | None | None |
| chr19 | 47388615 | 22.47 | NM_008018 | Sh3pxd2a | None | None |
| chr19 | 47388661 | 24.44 | NM_008018 | Sh3pxd2a | None | None |
| chr2 | 5636284 | 11.52 | NM_177343 | Camkid | None | None |
| chr2 | 37649110 | 20.86 | NM_001163566 | Crb2 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr2 | 37649121 | 20.12 | NM_001163566 | Crb2 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr2 | 76176253 | 15.65 | NM_001081033 | Pdella | Mtf2 | |
| chr2 | 91316809 | –23.84 | NM_172668 | Lrp4 | None | None |
| chr2 | 91475664 | 16.00 | NM_010168 | F2 | None | None |
| chr2 | 126379285 | –22.21 | NM_011978 | Slc27a2 | None | None |
| chr2 | 147874612 | –14.49 | NM_010446 | Foxa2 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr2 | 165242677 | 16.72 | NM_054055 | Slc13a3 | None | None |
| chr3 | 69120629 | –12.04 | NM_178726 | Ppm11 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr3 | 89229249 | 12.43 | NM_001113331 | Shc1 | None | None |
| chr3 | 128906125 | 15.67 | NM_011098 | Pitx2 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr3 | 151928358 | –26.03 | NM_199465 | Nexn | Mtf2, Jarid2, EZH2, Suz12 | |
| chr4 | 46728412 | –11.11 | NM_001081141 | Gabbr2 | None | None |
| chr4 | 65065259 | –33.06 | NM_019514 | Astn2 | None | None |
| chr4 | 80557862 | 10.89 | NM_026821 | Lurap11 | None | None |
| chr4 | 117928909 | 15.15 | NM_011213 | Ptprf | None | None |
| chr4 | 124682634 | –26.36 | NM_138683 | Rspo1 | None | None |
| chr4 | 133430503 | –18.16 | NM_001285506 | Rps6ka1 | None | None |
| chr4 | 134711341 | 26.82 | NM_019732 | Runx3 | Suz12 | |
| chr4 | 134711350 | 23.31 | NM_019732 | Runx3 | Suz12 | |
| chr4 | 139379960 | –22.47 | NM_011039 | Pax7 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr4 | 141640595 | –21.15 | NM_145402 | GM10565 | None | None |
| chr4 | 148423617 | 29.44 | NM_019781 | Pex14 | None | None |
| chr4 | 149745860 | 17.35 | NM_001085492 | Rere | None | None |
| chr4 | 151089350 | 26.29 | NM_001081557 | Camta1 | None | None |
| chr4 | 152834168 | 18.58 | NM_001099299 | Ajap1 | None | None |
| chr5 | 34066416 | 11.04 | NM_001163217 | Fgfr3 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr5 | 37187480 | 10.53 | NM_026242 | Mrfap1 | None | None |
| chr5 | 114723943 | –11.11 | NM_148935 | Foxn4 | None | None |
| chr5 | 122278672 | 22.15 | NM_001306126 | Sh2b3 | Mtf2 | |
| chr5 | 131782939 | –23.02 | NM_145218 | Wbscr17 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr5 | 140447989 | 17.64 | NM_175522 | Rlfn1 | None | None |
| chr5 | 148138165 | –13.33 | NM_001039678 | Urad | None | None |
| chr6 | 23210525 | –18.28 | NM_028462 | Cadps2 | Mtf2 | |
| chr6 | 63207478 | 17.79 | NM_008167 | Grid2 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr6 | 83135914 | –26.38 | NM_007835 | Dctn1 | None | None |
| chr6 | 85324297 | –10.98 | NM_001003955 | Rab11fip5 | None | None |
| chr6 | 98926364 | 30.44 | NM_001197322 | Foxp1 | None | None |
| chr6 | 113342775 | 33.59 | NM_133923 | Tt113 | None | None |
| chr6 | 125262312 | –21.28 | NM_010736 | Tltpr | Mtf2 | |
| chr7 | 13628786 | –15.20 | NM_145819 | Mzf1 | Suz12, Mtf2 | |
| chr7 | 16726237 | –11.83 | NM_148946 | Slc8a2 | None | None |
| chr7 | 24096775 | –16.75 | NM_001004194 | Nirpfe | None | None |
| chr7 | 29606786 | –24.74 | NM_016772 | Hnrnpl | None | Ebf1 |
| chr7 | 35015176 | 13.38 | NM_008155 | Gpi1 | None | None |
| chr7 | 52940127 | 18.03 | NM_001289693 | Sec1/Ntn5 | None | None |
| chr7 | 63520836 | –24.05 | NM_021879 | Oca2 | None | None |
| chr7 | 87481393 | –12.53 | NM_133952 | Unc45a | None | None |
| chr7 | 93301399 | 28.53 | NM_001102578 | Vmn2r75 | None | None |
| chr7 | 104376316 | 21.11 | NM_001177412 | Gab2 | None | None |
| chr7 | 133957534 | 27.42 | NM_026884 | Fam57b | None | ATOH1 |
| chr7 | 138078229 | –22.20 | NM_019564 | Htra1 | Mtf2, EZH2, Suz12 | |
| chr8 | 12430585 | –10.48 | NM_009233 | GM5607 | Mtf2 | |
| chr8 | 72406588 | 18.95 | NM_026818 | Cilp2 | Mtf2, Jarid2, EZH2, Suz12 | |
| chr8 | 72898699 | 14.06 | NM_016685 | Comp | Mtf2, EZH2, Suz12 | |
| chr8 | 73296263 | –11.49 | NM_008841 | Pik3r2 | None | None |
| chr8 | 83263159 | –24.64 | NM_053124 | Smarca5 | None | None |
| chr8 | 94882246 | –12.94 | NM_018826 | Irx5 | Mtf2, EZH2, Suz12 | |
| chr8 | 107880886 | –12.28 | NM_001081332 | Slc9a5 | None | None |
| chr8 | 116729816 | 13.57 | NM_173016 | Vat1l | Mtf2, Suz12 | |
| chr8 | 121971793 | –19.02 | NM_054095 | Necab2 | Jarid2, EZH2, Suz12 | |
| chr8 | 125088900 | 26.17 | NM_026014 | Cdt1 | None | Ebf1 |
| chr8 | 125389116 | –36.05 | NM_007662 | Cadherin 15 | None | Ebf1 |
| chr8 | 125389194 | –30.65 | NM_007662 | Cadherin 15 | None | Ebf1 |
| chr8 | 125389244 | –29.38 | NM_007662 | Cadherin 15 | None | Ebf1 |
| chr8 | 125389246 | –28.44 | NM_007662 | Cadherin 15 | None | Ebf1 |
| chr9 | 21549579 | 12.84 | NM_026282 | Ldlr | None | None |
| chr9 | 31720357 | –14.51 | NM_013800 | Barx2 | Jarid2, EZH2, Suz12 | |
| chr9 | 56994574 | –14.04 | NM_028347 | Neil1 | None | None |
| chr9 | 107611227 | –21.43 | NM_011349 | Sema3f | Mtf2, EZH2, Suz12 | |
| chrX | 11655662 | –14.96 | NM_029510 | Bcor | Mtf2, Jarid2, EZH2, Suz12 | |
| chrX | 11658411 | –23.91 | NM_175046 | Bcor | Mtf2, Jarid2, EZH2, Suz12 | |
| chrX | 34415040 | 22.79 | NM_019668 | Ube2a | None | None |
| chrX | 34415077 | 21.67 | NM_019668 | Ube2a | None | None |
| chrX | 56387270 | 27.18 | NM_010200 | Fgf13 | Mtf2, EZH2 | |
| chrX | 68917537 | –24.71 | NM_010340 | Gpr50 | Mtf2, Jarid2, EZH2, Suz12 | |
| chrX | 97454071 | 21.48 | NM_001177943 | Eda | None | None |
| chrX | 110412278 | 23.36 | NM_033605 | Dach2 | None | None |
| chrX | 130221716 | 30.33 | NM_001105245 | Pcdh19 | Mtf2, Jarid2, Suz12 | |
| chrX | 158346841 | –25.22 | NM_198409 | Nhs | None | None |
| chrX | 160347121 | 27.82 | NM_001290379 | Ap1s2 | None | None |