Table 2 Pathway classification of differentially methylated genes in melanoma

Tumor suppressors

CDH1 (88%), CDKN2A (76%), PTEN (23%), APC (15%), SOCS1 (75%)

[15, 40, 151, 152]

Oncogenes

PAX7 (31%), OLIG2 (63%), SYK (2%)

[35, 40]

Protein kinases

DAPK1 (19%), HSPB8 (69%)

[152, 153]

Differentiation

TNFRSF10A/C/D,CCR7, THBD (20%), BST2 (50%), DPP4 (80%), ENC1 (6%), GDF15 (75%), WIF1

[35, 154–159]

Homeodomain proteins

HOXB13 (20%), PAX2 (38%), PAX7 (31%), NKX2-3 (63%)

[35, 40, 160]

Hypoxia

CDKN1B, CDKN1C (35%), CXCR4, LXN (95%)

[35, 36, 151, 154]

Transcription factors

PGR (56%), HAND1/2 (15%), PAX7 (31%), ESR1, RUNX3 (23%)

[40, 151, 161]

Interferon gamma response

SOCS1 (75%), HLA-A, PTGS2 (20%), SOCS3 (60%), BST2 (50%), XAF1, SOCS2 (44%)

[35, 152, 162–164]

Epithelial-to-mesenchymal transition

TFPI2, TIMP3 (13%), COL1A2 (63%), TPM1 (8%), PDLIM4

[39, 42, 152, 165, 166]

PI3K/mTOR

CXCR4, CDKN1B, PTEN (23%)

[151, 154]

Metastasis

CDH8 (10%), CDH13 (44%), EPB41L3 (5%), SERPINB5 (100%), TFPI2, SYK (3%), CCR7

[35, 40, 152, 154, 155]

Immune recognition

MAGE-A1,2,3,4, BAGE (83%), HLA-A

[167, 168]

Apoptosis

RASSF1A, HSPB6 (69%), TRAILR1 (80%)

[39, 169, 170]

DNA repair

MGMT (0–50%)

[151]

Metabolism

CYP1B1 (100%), DNAJC15 (50%), CD98

[35, 43, 171]

Other/unknown

FAM78A, LRRC2, PCSK1, PPP1R3C, PTPRG, QPCT, SLC27A3, DERL3, MFAP2, MT1G, WFDC1

[35, 39, 42, 151]