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Table 2 Pathway classification of differentially methylated genes in melanoma

From: Aberrant DNA methylation in melanoma: biomarker and therapeutic opportunities

Pathway/function Genes (methylation frequencya) References
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, 154159]
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, 162164]
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]
  1. aWhere applicable