Table 2.
Weights based on 208 breast cancer cases from the Polish breast cancer study for the 57 genes identified from methylation analysis that have corresponding mRNA expression data and used as weighting factors for calculation of prognostic signature
| Gene | Gene name | weights |
|---|---|---|
| DNALI1 | dynein, axonemal, light intermediate chain 1 | 0.7370 |
| CALML5 | calmodulin-like 5 | 0.6845 |
| HCLS1 | hematopoietic cell-specific Lyn substrate 1 | 0.6748 |
| SERPINA5 | serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5 | 0.6397 |
| PDZK1 | PDZ domain containing 1 | 0.6325 |
| AGR3 | anterior gradient 3 | 0.6307 |
| PLAT | plasminogen activator, tissue | 0.6215 |
| SCUBE2 | signal peptide, CUB domain, EGF-like 2 | 0.6146 |
| KYNU | kynureninase | 0.6116 |
| SCNN1A | sodium channel, non-voltage-gated 1 alpha subunit | 0.5683 |
| SPOCK2 | sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2 | 0.5480 |
| REEP6 | receptor accessory protein 6 | 0.5400 |
| STC2 | stanniocalcin 2 | 0.5338 |
| C8orf4 | chromosome 8 open reading frame 4 | 0.5319 |
| CAP2 | CAP, adenylate cyclase-associated protein, 2 (yeast) | 0.5118 |
| CFB | complement factor B | 0.5039 |
| C1orf64 | chromosome 1 open reading frame 64 | 0.5024 |
| IL20 | interleukin 20 | 0.4972 |
| CD247 | CD247 molecule | 0.4967 |
| FABP7 | fatty acid binding protein 7, brain | 0.4952 |
| CCND1 | cyclin D1 | 0.4827 |
| AKR7A3 | aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase) | 0.4678 |
| TFF1 | trefoil factor 1 | 0.4575 |
| TAP1 | transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) | 0.4360 |
| ZG16B | zymogen granule protein 16B | 0.4226 |
| MMP7 | matrix metallopeptidase 7 (matrilysin, uterine) | 0.3514 |
| HMGCS2 | 3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial) | 0.3425 |
| CAMK2N1 | calcium/calmodulin-dependent protein kinase II inhibitor 1 | 0.3393 |
| GZMA | granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3) | 0.3298 |
| ATP6V1B1 | ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1 | 0.3214 |
| GLIPR2 | GLI pathogenesis-related 2 | 0.3054 |
| PRSS8 | protease, serine, 8 | 0.2737 |
| MLPH | melanophilin | 0.2733 |
| C10orf116 | adipogenesis regulatory factor | 0.2715 |
| THRSP | thyroid hormone responsive | 0.2706 |
| CRYAB | crystallin, alpha B | 0.2598 |
| ALOX5AP | arachidonate 5-lipoxygenase-activating protein | 0.2439 |
| IFITM3 | interferon induced transmembrane protein 3 | 0.2414 |
| CD248 | CD248 molecule, endosialin | 0.2359 |
| CXCL12 | chemokine (C-X-C motif) ligand 12 | 0.2344 |
| SERPINA3 | serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 | 0.2328 |
| CILP | cartilage intermediate layer protein, nucleotide pyrophosphohydrolase | 0.2233 |
| CST3 | cystatin C | 0.2154 |
| HLA-DRA | major histocompatibility complex, class II, DR alpha | 0.2039 |
| SCGB3A1 | secretoglobin, family 3A, member 1 | 0.1925 |
| S100A7 | S100 calcium binding protein A7 | −0.1892 |
| SLPI | secretory leukocyte peptidase inhibitor | 0.1823 |
| GP1BB | glycoprotein Ib (platelet), beta polypeptide | −0.1781 |
| S100A9 | S100 calcium binding protein A9 | 0.1761 |
| CCL8 | chemokine (C-C motif) ligand 8 | −0.1726 |
| SMOC2 | SPARC related modular calcium binding 2 | 0.1738 |
| TFF3 | trefoil factor 3 (intestinal) | 0.1617 |
| MSLN | mesothelin | 0.1611 |
| MUC1 | mucin 1, cell surface associated | 0.1539 |
| PRSS23 | protease, serine, 23 | 0.1518 |
| TMEM119 | transmembrane protein 119 | 0.1026 |
| PI15 | peptidase inhibitor 15 | 0.1024 |
*These genes had more than one methylation marker associated with the mRNA expression target and the average of the sites was used to calculate the weighted Rho value.