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. 2018 Feb 1;41(5):2687–2703. doi: 10.3892/ijmm.2018.3448

Table III.

DMRs between fibroblast groups.

A, Hyper-methylated genes in MAF vs. CDF
RefSeq ID Entrez Gene ID Symbol Definition Descriptive GO BP term FDR CDF M-value MAF M-value ACF M-value
NM_001141945 59 ACTA2 Actin, α2, smooth muscle, aorta GO:0090131 6.0E-07 −3.48 3.43 1.72
NM_006308 8988 HSPB3 Heat shock 27 kDa protein 3 – 7.6E-07 −3.32 3.07 2.09
NM_001202233 3164 NR4A1 Nuclear receptor subfamily 4. group A, member 1 GO:0044344 7.6E-07 0.07 4.86 4.06
NM_031950 83888 FGFBP2 Fibroblast growth factor binding protein 2 – 7.6E-07 −3.13 1.69 −2.15
NM_001307983 130013 ACMSD Aminocarboxymuconate semialdehyde decarboxylase GO:1905004 7.6E-07 −2.15 3.15 1.12
NM_001256552 79661 NEIL1 Nei-like DNA glycosylase 1 GO:0010730 7.6E-07 −1.86 3.19 0.87
NM_001039469 2011 MARK2 MAP/microtubule affinity-regulating kinase 2 GO:0016055 7.6E-07 −3.05 1.15 1.01
NM_001193341 221421 RSPH9 Radial spoke head 9 homolog (Chlamydomonas) GO:0044458 7.6E-07 −3.74 0.46 −2.33
NM_033199 90226 UCN2 Urocortin 2 GO:0031669 7.6E-07 −3.43 1.19 0.14
B, Hypo-methylated genes in MAF vs. CDF
RefSeq ID Entrez Gene ID Symbol Definition Descriptive GO BP term FDR CDF M-value MAF M-value ACF M-value
NM_001199505 116154 PHACTR3 Phosphatase and actin regulator 3 GO:0043086 7.6E-07 3.37 −2.73 0.74
NM_144719 152206 CCDC 13 Coiled-coil domain containing 13 GO:0035058 7.6E-07 2.05 −2.57 −0.17
NM_000438 5077 PAX3 Paired box 3 GO:0009887a 7.6E-07 2.96 −1.53 2.98
NM_002151 3249 HPN Hepsin GO:0010719 7.6E-07 4.09 −1.15 1.34
NM_153038 151278 CCDC 140 Coiled-coil domain containing 140 – 7.6E-07 2.40 −2.86 2.87
NM_000384 338 APOB Apolipoprotein B GO:0032496a 7.6E-07 2.90 −2.93 0.66
C, Hyper-methylated genes in MAF vs. ACF
RefSeq ID Entrez Gene ID Symbol Definition Descriptive GO BP term FDR CDF M-value MAF M-value ACF M-value
NM_001242805 676 BRDT Bromodomain, testis-specific GO:0006338 4.2E-06 1.15 3.62 −1.43
NM_001300905 11176 BAZ2A Bromodomain adjacent to zinc finger domain, 2A GO:0006338 5.1E-06 −4.52 −0.9 −4.29
NM_018593 117247 SLC16A10 Solute carrier family 16 (aromatic amino acid transporter). Member 10 GO:0006865 4.2E-06 −3.50 1.46 −3.98
NM_005992 6899 TBX1 T-box 1 GO:0001525 4.2E-06 0.79 1.60 −2.20
NM_178818 146223 CMTM4 CKLF-like MARVEL transmembrane domain containing 4 GO:0005125 4.2E-06 −2.70 1.35 −2.46
NM_000663 18 ABAT 4-aminobutyrate aminotransferase GO:0001666a 4.2E-06 −4.14 −0.07 −4.11
NM_006829 10974 ADIRF Adipogenesis regulatory factor GO:0030154 4.2E-06 −4.29 0.31 −4.32
NM_006181 4917 NTN3 Netrin 3 GO:0007411 4.2E-06 −4.54 −1.14 −4.78
NM_031950 83888 FGFBP2 Fibroblast growth factor binding protein 2 – 4.7E-06 −3.13 1.69 −2.15
NM_001720 656 BMP8B Bone morphogenetic protein 8b GO:0001503a 4.7E-06 −4.66 −0.79 −4.55
NM_005731 10109 ARPC2 Actin related protein 2/3 complex. subunit 2, 34 kDa GO:1900026 5.1E-06 −3.37 −0.84 −4.31
D, Hypo-methylated genes in MAF vs. ACF
RefSeq ID Entrez Gene ID Symbol Definition Descriptive GO BP term FDR CDF M-value MAF M-value ACF M-value
NM_000192 6910 TBX5 T-box 5 GO:0002009a 1.3E-06 −2.27 −3.24 3.75
NM_153038 151278 CCDC 140 Coiled-coil domain containing 140 – 3.4E-06 2.40 −2.86 2.87
NM_000438 5077 PAX3 Paired box 3 GO:0009887a 4.2E-06 2.96 −1.53 2.98
NM_001053 6755 SSTR5 Somatostatin receptor 5 GO:0007186 4.2E-06 −0.75 −4.83 −0.62
NM_152739 3205 HOXA9 Homeobox A9 GO:0007275 4.2E-06 0.09 −3.76 0.28
NM_015916 51063 C ALHM2 Calcium homeostasis modulator 2 GO:0005261 5.1E-06 −4.79 −4.84 −1.16
E, Hyper-methylated genes in ACF vs. CDF
RefSeq ID Entrez Gene ID Symbol Definition Descriptive GO BP term FDR CDF M-value MAF M-value ACF M-value
NM_000192 6910 TBX5 T-box 5 GO:0002009a 3.6E-06 −2.27 −3.24 3.75
NM_001141945 59 ACTA2 Actin. α2, smooth muscle, aorta GO:0090131 3.6E-06 −3.48 3.43 1.72
NM_006308 8988 HSPB3 Heat shock 27 kDa protein 3 – 3.6E-06 −3.32 3.07 2.09
NM_001039469 2011 MARK2 MAP/microtubule affinity-regulating kinase 2 GO:0016055 3.6E-06 −3.05 1.15 1.01
NM_001202233 3164 NR4A1 Nuclear receptor subfamily 4. group A. member 1 GO:0044344 4.0E-06 0.07 4.86 4.06
NM_000129 2162 F13A1 Coagulation factor XIII. A1 polypeptide GO:0007596 4.0E-06 −4.97 −0.78 −1.12
NM_001286555 56940 DUSP22 Dual specificity phosphatase 22 GO:0008283 5.9E-06 −3.92 −0.45 −0.51
NM_015916 51063 CALHM2 Calcium homeostasis modulator 2 GO:0005261 5.9E-06 −4.79 −4.84 −1.16
NM_001012631 9235 IL32 Interleukin 32 GO:0005125 5.9E-06 −3.35 0.37 1.29
NM_000504 2159 F10 Coagulation factor X GO:0030335a 6.2E-06 −0.42 3.59 3.68
F, Hypo-methylated genes in ACF vs. CDF
RefSeq ID Entrez Gene ID Symbol Definition Descriptive GO BP term FDR CDF M-value MAF M-value ACF M-value
NM_001297436 3036 HAS1 Hyaluronan synthase 1 GO:0085029 4.0E-06 1.38 −4.34 −4.22
NM_000965 5915 RARB Retinoic acid receptor, beta GO:0007165 4.0E-06 −0.57 −4.43 −4.66
NM_001166247 2898 GRIK2 Glutamate receptor, ionotropic, kainate 2 GO:0046328 4.0E-06 0.73 −3.46 −3.40
NM_001207011 1271 CNTFR Ciliary neurotrophic factor receptor GO:0060538 5.8E-06 2.87 −2.6 −1.69
NM_001128423 255027 MPV17L MPV17 mitochondrial membrane protein-like GO:0010730 6.3E-06 −0.75 −3.91 −4.53

The 15 most marked DMRs with FDR<0.1 and |log2FC|>1 are listed.

a

Listed among GO terms enriched by differentially expressed genes as identified by gene set enrichment analysis. DMR, differentially methylated genomic region; FDR, false discovery rate; M-value, methylation M-value; GO BP, gene ontology biological process; MAF, melanoma-associated fibroblast; ACF, autologous control fibroblast; CDF, control dermal fibroblast.