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Table 2 Top 20 CpG sites by magnitude of DNA methylation difference between subcutaneous and omental adipose tissue at each time point

From: Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

Illumina probe ID T statistic Adjusted P value AB mean beta OM mean beta Δbeta CpG site chromosome and positiona UCSC gene namea b Location Rank P valuec Rank biomarkerd
Before weight loss
 cg02245004 −14.92 2.32E−04 0.12 0.64 −0.51 15:76634887 Intergenic   318 1
 cg20540209 −13.61 7.74E−04 0.06 0.53 −0.48 15:76633981 ISL2 Body 557 NA
 cg17446010 −16.17 7.97E−05 0.13 0.58 −0.45 15:76633627 ISL2 Body 192 NA
 cg00838040 −18.85 1.02E−05 0.53 0.96 −0.43 16:84446919 ATP2C2 Body 66 NA
 cg03923561 23.49 5.10E−07 0.45 0.04 0.41 12:54447220 HOXC4 5′UTR;TSS1500 12 2
 cg09400037 −17.63 2.50E−05 0.42 0.82 −0.40 16:84822801 Intergenic   102 4
 cg22747076 20.83 2.62E−06 0.42 0.02 0.40 12:54447873 HOXC4 1stExon;Body 31 3
 cg15233062 22.19 1.11E−06 0.48 0.09 0.39 12:54447349 HOXC4 5′UTR;TSS1500 18 NA
 cg00108351 −16.19 7.79E−05 0.23 0.61 −0.39 16:86529658 Intergenic   191 NA
 cg01184975 23.53 4.97E−07 0.44 0.06 0.39 12:114852091 Intergenic   11 NA
 cg12984729 −13.17 1.19E−03 0.12 0.50 −0.38 15:76633817 ISL2 Body 668 13
 cg08307030 −10.46 2.27E−02 0.14 0.52 −0.38 15:76634380 ISL2 3′UTR 2336 16
 cg20291855 −20.02 4.48E−06 0.02 0.40 −0.38 4:13524143 Intergenic   41 NA
 cg11797364 −14.85 2.46E-04 0.59 0.97 −0.38 6:436969 Intergenic   329 6
 cg01697719 12.27 2.97E-03 0.38 0.01 0.37 22:19754125 TBX1 Body 986 NA
 cg07266404 28.62 3.38E−08 0.43 0.07 0.37 12:54447584 HOXC4 5′UTR;TSS200 4 NA
 cg24864887 −13.27 1.07E−03 0.14 0.50 −0.36 15:76635638 Intergenic   644 NA
  cg21215550 18.67 1.15E−05 0.55 0.20 0.36 9:969544 Intergenic   70 NA
 cg06800235 16.38 6.67E−05 0.56 0.20 0.35 1:7692367 CAMTA1 Body 176 NA
 cg08036309 −21.31 1.92E−06 0.17 0.52 −0.35 4:13536991 Intergenic   24 NA
After weight loss
 cg00838040 −38.29 6.04E−10 0.34 0.97 −0.64 16:84446919 ATP2C2 Body 2 1
 cg09400037 −34.83 2.24E−09 0.33 0.92 −0.59 16:84822801 Intergenic   3 NA
 cg02245004 −11.25 9.01E−03 0.07 0.65 −0.58 15:76634887 Intergenic   4290 NA
 cg20540209 −10.86 1.41E−02 0.02 0.59 −0.56 15:76633981 ISL2 Body 4998 NA
 cg22747076 17.06 3.89E−05 0.59 0.06 0.53 12:54447873 HOXC4 1stExon;Body 517 NA
  cg24145118 11.73 5.30E−03 0.84 0.31 0.52 10:2777041 Intergenic   3554 NA
 cg17446010 −12.37 2.68E−03 0.09 0.61 −0.52 15:76633627 ISL2 Body 2760 NA
 cg03923561 14.78 2.62E−04 0.60 0.09 0.51 12:54447220 HOXC4 5′UTR;TSS1500 1131 NA
 cg21917524 −28.43 3.70E−08 0.31 0.81 −0.51 11:74200334 Intergenic   19 2
 cg00108351 −11.97 4.11E−03 0.17 0.67 −0.51 16:86529658 Intergenic   3233 NA
 cg12984729 −11.88 4.50E−03 0.09 0.58 −0.49 15:76633817 ISL2 Body 3338 4
 cg15233062 14.15 4.63E−04 0.62 0.14 0.49 12:54447349 HOXC4 5′UTR;TSS1500 1400 NA
 cg00319661 17.95 1.96E−05 0.92 0.43 0.49 5:2632178 Intergenic   381 NA
 cg11797364 −21.71 1.49E−06 0.47 0.93 −0.47 6:436969 Intergenic   122 NA
 cg13593391 12.35 2.74E−03 0.94 0.47 0.47 11:132582488 OPCML Body 2783 NA
 cg08307030 −10.93 1.30E−02 0.14 0.60 −0.46 15:76634380 ISL2 3′UTR 4855 NA
  cg08773462 −11.52 6.65E−03 0.10 0.56 −0.46 16:17107610 Intergenic   3864 NA
 cg01697719 16.48 6.15E−05 0.49 0.03 0.45 22:19754125 TBX1 Body 622 NA
 cg20249252 15.65 1.22E−04 0.60 0.15 0.45 12:114852308 Intergenic   837 NA
 cg17185060 −17.72 2.34E−05 0.27 0.72 −0.45 3:193990712 Intergenic   415 NA
  1. Illumina probe IDs in bold indicate probes unique to the analysis at that time point
  2. aGene symbol and map position as Illumina manifest, GRCh37/hg19
  3. b‘Intergenic’, no gene loci annotation in Illumina manifest
  4. c P value in ‘traditional’ differential methylation analysis
  5. dIndicates ranking in combinatorial analysis if applicable. NA indicates that the CpG site was not seen in this analysis
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Clinical Epigenetics

ISSN: 1868-7083

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