Table 4.
Genomic information and reason for inclusion in the original 422-gene signature for the 34 genes selected in the prediction model
| Annotation | Expression | Copy number | DNA Methylation | miRNA expression | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Symbol | Name | Entrez-ID | chr | Start | Length | Fold-change (CR/IR) | Presence | cytoband | Methylated Genes | Methylation Status (CR/IR) | miRNA | CR/IR expression |
| LRRC8D | leucine rich repeat containing 8 family, member D | 55144 | 1 | 90286572 | 115417 | 1.13 | ||||||
| OLFML3 | olfactomedin-like 3 | 56944 | 1 | 114522029 | 2846 | 0.76 | ||||||
| DPT | dermatopontin | 1805 | 1 | 168664694 | 33748 | 0.9 | ||||||
| FAP | fibroblast activation protein, alpha | 2191 | 2 | 163027199 | 72846 | 0.7 | ||||||
| RNF13 | ring finger protein 13 | 11342 | 3 | 149530474 | 149451 | Gain | 3q22.1-q29 | CRKRS | 1.19 | |||
| SLC7A11 | solute carrier family 7, (cationic amino acid transporter, y + system) member 11 | 23657 | 4 | 139085247 | 78256 | Loss | 4q13.3-q35.2 | |||||
| TRIO | triple functional domain (PTPRF interacting) | 7204 | 5 | 14143828 | 365630 | 1.18 | Gain | 5p15.33-p13.1 | ||||
| DROSHA | drosha, ribonuclease type III | 29102 | 5 | 31400601 | 131681 | 1.16 | Gain | 5p15.33-p13.1 | ||||
| RPS23 | ribosomal protein S23 | 6228 | 5 | 81569138 | 5097 | 0.96 | Loss | 5q11.2-q21.1 | UNQ9217 | 1.15 | miR-22 | 0.8 |
| SYNE1 | spectrin repeat containing, nuclear envelope 1 | 23345 | 6 | 152442821 | 196658 | Loss | 6q15-q27 | LAD1, NFATC2, SLC1A2, STEAP4 | 0.77 | miR-22, miR-200b | 1.22 | |
| STEAP4 | STEAP family member 4 | 79689 | 7 | 87905743 | 30466 | SYNE1 | 0.82 | |||||
| PRSS1 | protease, serine, 1 (trypsin 1) | 5644 | 7 | 142457318 | 3609 | 1.32 | Gain | 7q32.1-q36.3 | ||||
| PRSS2 | protease, serine, 2 (trypsin 2) | 5645 | 7 | 142479907 | 1471 | 1.34 | Gain | 7q32.1-q36.3 | ||||
| ST18 | suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein) | 9705 | 8 | 53023391 | 299048 | 0.97 | Gain | 8p11.21-q24.3 | ||||
| RPS20 | ribosomal protein S20 | 6224 | 8 | 56980738 | 6402 | Gain | 8p11.21-q24.3 | miR-135b | 1.22 | |||
| ZBTB10 | zinc finger and BTB domain containing 10 | 65986 | 8 | 81398447 | 36163 | 1.2 | Gain | 8p11.21-q24.3 | miR-708 | 1.2 | ||
| MTAP | methylthioadenosine phosphorylase | 4507 | 9 | 21802634 | 63335 | 1.12 | Loss | 9p21.3-p21.2 | ||||
| GCNT1 | glucosaminyl (N-acetyl) transferase 1, core 2 | 2650 | 9 | 79056581 | 65751 | 1.17 | ||||||
| C10orf26 | WBP1L - chromosome 10 open reading frame 26 | 54838 | 10 | 104503726 | 72295 | 0.87 | No | |||||
| MYO7A | myosin VIIA | 4647 | 11 | 76839309 | 86977 | 1.08 | Gain | 11q13.5-q14.1 | ||||
| PDGFD | platelet derived growth factor D | 80310 | 11 | 103777913 | 257114 | 0.76 | No | |||||
| KLRAP1 | killer cell lectin-like receptor subfamily A pseudogene 1 | 10748 | 12 | 10741076 | 11358 | Gain | 12p13.33-p11.21 | miR-22 | 0.8 | |||
| NUAK1 | NUAK family, SNF1-like kinase, 1 | 9891 | 12 | 106457124 | 76687 | 0.75 | No | |||||
| POLE | polymerase (DNA directed), epsilon | 5426 | 12 | 133200347 | 63598 | 1.14 | No | |||||
| ENTPD5 | ectonucleoside triphosphate diphosphohydrolase 5 | 957 | 14 | 74433180 | 52846 | 1.13 | No | |||||
| THBS1 | thrombospondin 1 | 7057 | 15 | 39873279 | 16389 | Loss | 15q11.1-q21.1 | CORO6, LAD1, NFATC2, SLC1A2, SNAI1 | 0.74 | miR-22, miR-641, miR-200b | 1.22 | |
| CCPG1 | cell cycle progression 1 | 9236 | 15 | 55647437 | 53137 | 0.84 | Loss | 15q21.3 | ||||
| PDPR | pyruvate dehydrogenase phosphatase regulatory subunit | 55066 | 16 | 70147528 | 47656 | 1.04 | Loss | 16q12.2-q24.3 | ||||
| RHOT1 | ras homolog gene family, member T1 | 55288 | 17 | 30469472 | 83274 | 0.87 | Gain | 17p13.3-q21.2 | ||||
| MLX | MAX-like protein X | 6945 | 17 | 40719077 | 6144 | 0.88 | No | |||||
| COPZ2 | coatomer protein complex, subunit zeta 2 | 51226 | 17 | 46103532 | 11620 | 0.78 | No | |||||
| MATK | megakaryocyte-associated tyrosine kinase | 4145 | 19 | 3777966 | 8449 | 0.93 | No | |||||
| TIMP3 | TIMP metallopeptidase inhibitor 3 | 7078 | 22 | 33196801 | 62227 | 0.7 | Loss | 22q11.22 | miR-22 | 0.8 | ||
| MCM5 | minichromosome maintenance complex component 5 | 4174 | 22 | 35796115 | 24380 | 1.19 | Loss | 22q11.22-q13.33 | ||||
In the Expression, Copy number, DNA methylation, and miRNA expression, only those with significant differential values between CR and IR were represented. Some genes had more than one biological difference
Copy number shows the chromosomal region (cytoband) that was significantly correlated with gene expression in the 422-gene signature. DNA Methylation and miRNA expression shows the initial variables that were significantly correlated to gene expression in the 422-gene signature