Table 1.
Overview of the technically validated targets, deduced from the targeted DNA methylation microarray experiments. Technical validation of the targets was undertaken with methylation-sensitive restriction enzyme high-throughput quantitative polymerase chain reaction (MSRE-HT-qPCR) and confirmed 25 genes for the comparison tumour vs. PBMC and 19 genes for the comparison tumour vs. adjacent tissue. Differential methylation for both comparisons was found for 17 targets. PBMC = peripheral blood mononuclear cell.
| Gene Symbol | Descirption | Tumour vs. PBMC | Tumour vs. Adjacent Tissue | ||||
|---|---|---|---|---|---|---|---|
| p-Value | FDR | log2-Fold-Change | p-Value | FDR | Log2-Fold-Change | ||
| ESR1 | Estrogen receptor 1 | <1 × 10−7 | <1 × 10−7 | 7 | <1 x10−7 | <1 × 10−7 | 4 |
| TFPI2 | Tissue factor pathway inhibitor 2 | <1 × 10−7 | <1 × 10−7 | 19 | 2.3 × 10−6 | 0.0000184 | 6 |
| WT1 | Wilms tumor 1 | <1 × 10−7 | <1 × 10−7 | 6 | 3.9 × 10−6 | 0.0000267 | 2 |
| TMEFF2 | Transmembrane protein with EGF-like and two follistatin-like domains 2 | <1 × 10−7 | <1 × 10−7 | 7 | <1 × 10−7 | <1 × 10−7 | 4 |
| PENK | Proenkephalin | <1 × 10−7 | <1 × 10−7 | 8 | 0.002722 | 0.0131 | 2 |
| MYOD1 | Myogenic differentiation 1 | <1 × 10−7 | <1 × 10−7 | 4 | |||
| TWIST1 | Twist homolog 1 (Drosophila) | <1 × 10−7 | <1 × 10−7 | 5 | <1 × 10−7 | <1 × 10−7 | 5 |
| DCC | Deleted in colorectal carcinoma | <1 × 10−7 | <1 × 10−7 | 12 | 0.014024 | 0.0449 | 4 |
| PTGS2 | Prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) | <1 × 10−7 | <1 × 10−7 | 12 | |||
| TJP2 | Tight junction protein 2 (zona occludens 2) | <1 × 10−7 | <1 × 10−7 | 15 | |||
| SPARC | Secreted protein, acidic, cysteine-rich (osteonectin) | 4.00 × 10−7 | 1.60 × 10−6 | 5 | |||
| PITX2 | Paired-like homeodomain 2 | 4.00 × 10−7 | 1.60 × 10−6 | 8 | <1 × 10−7 | <1 × 10−7 | 4 |
| SEZ6L | Seizure related 6 homolog (mouse)-like | 1.20 × 10−6 | 4.43 × 10−6 | 14 | 3.23 × 10−3 | 1.41 × 10−2 | 3 |
| DNAJC15 | DnaJ (Hsp40) homolog, subfamily C, member 15 | 1.40 × 10−6 | 4.50 × 10−6 | 11 | 1.71 × 10-2 | 5.11 × 10−2 | 5 |
| GDNF | Glial cell derived neurotrophic factor | 1.50 × 10−6 | 4.50 × 10−6 | 8 | 6.60 × 10−4 | 3.96 × 10−3 | 2 |
| CDX1 | Caudal type homeobox 1 | 1.50 × 10−6 | 4.50 × 10−6 | 3 | |||
| CLIC4 | 3.40 × 10−6 | 9.60 × 10−6 | 11 | 2.25 × 10−2 | 6.00 × 10−2 | 5 | |
| SFRP2 | Secreted frizzled-related protein 2 | 3.05 × 10−5 | 8.13 × 10−5 | 12 | 6.31 × 10−3 | 2.52 × 10−2 | 4 |
| HLA-G | Major histocompatibility complex, class I, G | 3.77 × 10−5 | 9.52 × 10−5 | 1 | 1.56 × 10−3 | 8.32 × 10−3 | 1 |
| GATA4 | GATA binding protein 4 | 7.86 × 10−5 | 1.89 × 10−4 | 3 | 1.81 × 10−2 | 5.11 × 10−2 | 1 |
| BOLL | Bol, boule-like (Drosophila) | 9.80 × 10−5 | 2.24 × 10−4 | 7 | 2.00 × 10−7 | 1.92 × 10−6 | 4 |
| THBD | Thrombomodulin | 1.65 × 10−4 | 3.60 × 10−4 | 8 | |||
| RARB | Retinoic acid receptor, beta | 9.28 × 10−4 | 1.94 × 10−3 | 7 | 9.12 × 10−3 | 3.13 × 10−2 | 5 |
| NKX2-1 | NK2 homeobox 1 | 6.80 × 10−3 | 1.36 × 10−2 | 3 | |||
| SALL3 | Sal-like 3 (Drosophila) | 2.63 × 10−2 | 5.05 × 10−2 | 4 | |||
| TCEB2 | Transcription elongation factor B (SIII), polypeptide 2 (18 kDa, elongin B) | 8.63 × 10−3 | 3.13 × 10−2 | 149 | |||
| S100A8 | S100 calcium binding protein A8 | 0.040431 | 0.102 | 1 | |||