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Table 1 Thirty-one differentially methylated and differentially expressed genes between the SK and SKTR models

From: Epigenetic silencing of TGFBI confers resistance to trastuzumab in human breast cancer

TargetID Chr Position Gene name Gene region SK SKTR SKTR vs SK
cg08757148 1 24513722 IL28RA;IL28RA;IL28RA 1stExon;1stExon;1stExon 0.11 0.67 0.56
cg03470088 1 24513939 IL28RA;IL28RA;IL28RA TSS200;TSS200;TSS200 0.05 0.79 0.75
cg26558485 1 47489282 CYP4X1;CYP4X1 1stExon;5′UTR 0.14 0.69 0.54
cg06816106 2 29033352 SPDYA;SPDYA TSS1500;TSS1500 0.18 0.64 0.46
cg14798656 2 97760745 FAHD2B TSS200 0.17 0.62 0.45
cg25999267 3 39424992 SLC25A38;SLC25A38 1stExon;5′UTR 0.19 0.75 0.56
cg17264618 3 40429014 ENTPD3 5′UTR 0.14 0.61 0.46
cg09363539 3 124931746 SLC12A8 TSS200 0.01 0.82 0.81
cg15860013 3 138327718 FAIM;FAIM;FAIM;FAIM;FAIM;FAIM;FAIM 5′UTR;TSS200;1stExon;5′UTR;1stExon;5′UTR;1stExon 0.18 0.68 0.50
cg20841906 3 160822911 B3GALNT1;B3GALNT1;B3GALNT1;B3GALNT1;B3GALNT1 5′UTR;5′UTR;5′UTR;5′UTR;TSS1500 0.06 0.70 0.64
cg20986370 4 57976171 IGFBP7 1stExon 0.19 0.69 0.49
cg19031658 4 74964856 CXCL2;CXCL2 1stExon;5′UTR 0.05 0.89 0.85
cg22847221 4 74964920 CXCL2;CXCL2 1stExon;5′UTR 0.13 0.61 0.48
cg00630212 4 74965135 CXCL2 TSS200 0.16 0.65 0.49
cg18804985 4 74965226 CXCL2 TSS1500 0.18 0.96 0.78
cg01429321 5 121413797 LOX;LOX 5′UTR;1stExon 0.10 0.62 0.52
cg21034676 5 135364552 TGFBI TSS200 0.11 0.61 0.51
cg14120129 5 135364575 TGFBI TSS200 0.06 0.61 0.55
cg09873933 5 135364580 TGFBI TSS200 0.09 0.63 0.54
cg07151644 6 31649089 LY6G5C TSS1500 0.16 0.60 0.44
cg07753583 7 150020206 LRRC61;ACTR3C;LRRC61 TSS200;5′UTR;TSS200 0.17 0.86 0.69
cg10348193 7 150020240 LRRC61;ACTR3C;LRRC61 TSS200;5′UTR;TSS200 0.15 0.97 0.82
cg11026333 7 150020269 LRRC61;ACTR3C;LRRC61 TSS200;5′UTR;TSS200 0.06 0.98 0.92
cg01270001 7 150020401 LRRC61;ACTR3C;LRRC61;LRRC61;LRRC61 1stExon;5′UTR;5′UTR;5′UTR;1stExon 0.13 0.94 0.81
cg22893248 7 150020751 ACTR3C;ACTR3C;LRRC61;LRRC61 1stExon;5′UTR;5′UTR;5′UTR 0.19 0.73 0.54
cg09327770 12 46663270 SLC38A1;SLC38A1 TSS200;TSS200 0.02 0.83 0.81
cg20463033 12 46663274 SLC38A1;SLC38A1 TSS200;TSS200 0.01 0.77 0.76
cg24795297 12 46663281 SLC38A1;SLC38A1 TSS200;TSS200 0.07 0.77 0.71
cg03859162 13 99404887 SLC15A1;SLC15A1 1stExon;5′UTR 0.12 0.66 0.55
cg03485262 14 92980031 RIN3 TSS200 0.04 0.72 0.68
cg08114373 14 92980204 RIN3;RIN3 5′UTR;1stExon 0.17 0.61 0.44
cg18614734 15 96876248 NR2F2;NR2F2;NR2F2;MIR1469;NR2F2 Body;Body;5′UTR;TSS1500;TSS1500 0.18 0.65 0.47
cg01549404 16 55358636 IRX6;IRX6 5′UTR;1stExon 0.11 0.61 0.50
cg01568244 16 67218584 KIAA0895L;EXOC3L TSS1500;Body 0.14 0.82 0.69
cg01666600 17 21279561 KCNJ12 TSS200 0.05 0.70 0.65
cg03928539 17 21279613 KCNJ12 TSS200 0.08 0.62 0.54
cg01637175 17 21281507 KCNJ12 5′UTR 0.08 0.78 0.70
cg11804833 17 40575289 PTRF;PTRF 1stExon;5′UTR 0.08 0.62 0.54
cg06093379 17 44896080 WNT3;WNT3 5′UTR;1stExon 0.01 0.83 0.82
cg24441185 18 9708096 RAB31 TSS200 0.06 0.92 0.86
cg17289202 18 56530789 ZNF532 5′UTR 0.13 0.80 0.67
cg22932336 19 4535070 PLIN5 5′UTR 0.10 0.88 0.78
cg04532834 19 4535188 PLIN5;PLIN5 1stExon;5′UTR 0.17 0.64 0.46
cg02505409 19 8429160 ANGPTL4;ANGPTL4;ANGPTL4;ANGPTL4 5′UTR;1stExon;5′UTR;1stExon 0.16 0.79 0.63
cg06837791 19 8429491 ANGPTL4;ANGPTL4 1stExon;1stExon 0.17 0.61 0.44
cg12831261 21 45078437 RRP1B;HSF2BP TSS1500;5′UTR 0.01 0.93 0.92
  1. *Italics denotes the three final genes selected for further analysis