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. 2016 Aug 18;59(11):2393–2405. doi: 10.1007/s00125-016-4074-5

Table 4.

A subset of differentially expressed genes accompanied by DMS in SAT between insulin-resistant vs insulin-sensitive womena

Probe Gene Relation to gene region DNA methylation Gene expression
IS average IR − IS p value T2Db,c [10] BMIb,d [20] GBPb,e [12] IS average IR/IS p value
cg07251857 ALPK3 1st exon 0.546 0.026 0.022 0.016 76 0.89 2.56 × 10−3
cg06532379 ALPK3 1st exon 0.193 0.039 0.015 0.015 76 0.89 2.56 × 10−3
cg14080050 B4GALT1 Body 0.447 −0.037 0.015 −0.014 228 1.10 1.48 × 10−3
cg13858803 B4GALT1 Body 0.566 0.027 0.040 0.027 228 1.10 1.48 × 10−3
cg00300298 BCL2L1 Body 0.251 −0.037 0.038 −0.019 151 1.07 2.01 × 10−3
cg12873919 BCL2L1 Body 0.504 −0.036 0.032 151 1.07 2.01 × 10−3
cg03290977 C1QTNF7 Body 0.247 −0.035 0.034 −0.024 44 0.86 3.28x10−3
cg01939704 C1QTNF7 Body 0.616 0.020 0.022 44 0.86 3.28 × 10−3
cg07538039 C1QTNF7 Body 0.610 0.025 0.021 44 0.86 3.28 × 10−3
cg06097727 C1QTNF7 Body 0.547 0.035 0.043 0.016 44 0.86 3.28 × 10−3
cg24829483 C1QTNF7 5′UTR 0.633 0.039 0.034 44 0.86 3.28 × 10−3
cg00545229 C1QTNF7 TSS200 0.563 0.041 0.018 44 0.86 3.28 × 10−3
cg15372098 C3orf26 Body 0.027 −0.016 0.014 69 0.92 3.98 × 10−4
cg00991994 C3orf26 Body 0.401 0.055 0.039 0.067 0.035 69 0.92 3.98 × 10−4
cg17351376 CD248 1st exon 0.504 0.019 0.032 239 1.42 1.03 × 10−3
cg07145284 CD248 TSS200 0.085 0.029 0.038 0.018 239 1.42 1.03 × 10−3
cg00350296 CD248 TSS1500 0.158 0.041 0.018 0.022 239 1.42 1.03 × 10−3
cg13860849 CD248 1st exon 0.191 0.054 0.002 0.015 239 1.42 1.03 × 10−3
cg10772263 CHST3 5′UTR 0.322 0.020 0.028 0.025 113 1.17 1.31 × 10−3
cg04268405 CHST3 TSS1500 0.369 0.042 0.024 0.219 113 1.17 1.31 × 10−3
cg12081643 COL4A1 3′UTR 0.670 −0.042 0.008 530 1.17 1.34 × 10−3
cg20818806 COL4A1 Body 0.299 0.042 0.019 530 1.17 1.34 × 10−3
cg02658690 COL4A1 Body 0.207 0.042 0.014 0.218 530 1.17 1.34 × 10−3
cg10908116 COL4A1 Body 0.247 0.043 0.017 0.053 0.026 530 1.17 1.34 × 10−3
cg02099572 COL4A1 Body 0.140 0.047 0.005 0.056 530 1.17 1.34 × 10−3
cg03430597 COL5A1 Body 0.751 0.018 0.004 0.018 162 1.10 5.97 × 10−4
cg24354213 COL5A1 Body 0.601 0.027 0.023 0.014 162 1.10 5.97 × 10−4
cg14274542 COL5A1 Body 0.596 0.037 0.019 0.012 162 1.10 5.97 × 10−4
cg10765212 COL5A2 TSS200 0.129 0.021 0.047 246 1.20 3.25 × 10−4
cg15194531 FMNL1 Body 0.466 0.041 0.005 0.018 165 1.09 5.32 × 10−4
cg08145262 FRS2 5′UTR 0.658 0.031 0.020 0.020 155 0.93 1.64 × 10−3
cg19563525 FRS2 5′UTR 0.382 0.035 0.006 0.017 155 0.93 1.64 × 10−3
cg10227830 GAB1 Body 0.272 0.039 0.016 141 0.89 1.53 × 10−4
cg25911551 GAB1 Body 0.494 0.046 0.049 0.019 141 0.89 1.53 × 10−4
cg08202226 GATAD2B TSS1500 0.793 −0.057 0.018 −0.029 282 0.94 3.97 × 10−3
cg05514401 IRS2 1st exon 0.792 0.031 0.002 0.028 242 0.85 1.24 × 10−3
cg11624345 KCNN4 Body 0.391 0.025 0.025 0.014 87 1.06 4.11 × 10−3
cg03731131 KCNN4 Body 0.378 0.032 0.039 87 1.06 4.11 × 10−3
cg22904711 KCNN4 Body 0.313 0.060 0.002 0.047 0.015 87 1.06 4.11 × 10−3
cg14616541 MYH10 Body 0.834 0.024 0.010 292 0.87 1.64 × 10−3
cg22588546 MYH10 Body 0.496 0.047 0.008 0.039 292 0.87 1.64 × 10−3
cg21542094 PFKFB3 TSS1500 0.081 −0.001 0.025 −0.013 542 0.80 5.53 × 10−5
cg00902516 PFKFB3 Body 0.739 0.020 0.019 0.016 542 0.80 5.53 × 10−5
cg03261682 PFKFB3 Body 0.780 0.028 0.006 0.026 542 0.80 5.53 × 10−5
cg05686026 PFKFB3 Body 0.683 0.045 0.001 0.033 542 0.80 5.53 × 10−5
cg03478610 PPP2R3A 5′UTR 0.871 −0.031 0.034 −0.014 91 0.93 1.49 × 10−3
cg00369142 PPP2R3A 3′UTR 0.378 0.044 0.013 0.060 0.025 91 0.93 1.49 × 10−3
cg11468953 PTPRJ Body 0.519 −0.039 0.027 −0.020 139 1.18 3.07 × 10−3
cg12124589 QSOX1 Body 0.775 −0.032 0.027 −0.020 175 1.08 1.70 × 10−3
cg09505809 QSOX1 TSS1500 0.179 0.039 0.031 175 1.08 1.70 × 10−3
cg00971364 RBMS3 TSS200 0.043 −0.018 0.034 381 0.90 5.14 × 10−4
cg23537305 RBMS3 Body 0.819 0.016 0.045 0.017 381 0.90 5.14 × 10−4
cg20299414 RBMS3 Body 0.729 0.035 0.018 0.013 381 0.90 5.14 × 10−4
cg27569887 RBMS3 3′UTR 0.698 0.043 0.026 381 0.90 5.14 × 10−4
cg16572224 SH3PXD2B Body 0.816 −0.049 0.002 −0.039 −0.019 145 1.13 4.76 × 10−3
cg05223396 SH3PXD2B Body 0.404 0.025 0.049 145 1.13 4.76 × 10−3
cg09744420 STX11 Body 0.654 0.041 0.002 0.020 356 0.89 2.98 × 10−3
cg19841369 SYNE2 Body 0.159 0.028 0.044 0.016 236 0.89 2.18 × 10−3
cg16725974 SYNE2 5′UTR 0.532 0.046 0.027 0.057 0.022 236 0.89 2.18 × 10−3
cg23250157 SYNE2 Body 0.756 0.061 0.018 236 0.89 2.18 × 10−3
cg18837713 ZDHHC17 Body 0.616 0.045 0.010 0.027 161 0.94 5.15 × 10−3

aDifferentially expressed genes (10% FDR) accompanied by DMS (p < 0.05) in SAT between insulin-resistant and insulin-sensitive women. Groups were compared using Limma and adjusting for BMI (gene expression, DMS) and age (DMS). This table contains a subset of the ESM Table 4 and focuses on DMS confirmed from the literature and mentioned in the discussion

bComparison with published transcriptome profiles on SAT from insulin-resistant vs insulin-sensitive individuals

cT2D vs control

dRegression coefficient

eAfter vs before bariatric surgery and weight loss

IR, insulin-resistant; IS, insulin-sensitive; T2D, type 2 diabetes