Table III.
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.
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.