Copy Number
The putative cancer-associated PDGs driven by SCNAs in each cancer type were identified by four criteria: 1) located in a peak region of a significantly recurrent focal SNCA locus estimated by the genomic identification of significant targets in cancer (GISTIC2) algorithm, (q≤0.25); 2) altered with high frequency and large amplitude (G-score ≥0.1); 3) mRNA reliably detected in at least 10% of tumor specimens in the given cancer type (90th percentile of FPKM value ≥1); and 4) mRNA significantly and positively correlated with copy numbers (Pearson P-value less than 0.001).
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| Overall_Gscore | No. of Cancer Types | ||||
| HGNC Symbol | Ensembl Gene ID | Amplification | Deletion | Amplification | Deletion |
| SMYD2 | ENSG00000143499 | 0.00 | 0.38 | 0 | 2 |
| SLC4A8 | ENSG00000050438 | 0.00 | 0.00 | 0 | 0 |
| MAPKAPK2 | ENSG00000162889 | 0.12 | 0.00 | 1 | 0 |
| STK4 | ENSG00000101109 | 0.14 | 0.00 | 1 | 0 |
| HSP90AB1 | ENSG00000096384 | 0.30 | 0.00 | 2 | 0 |
| HAO2 | ENSG00000116882 | 0.00 | 0.00 | 0 | 0 |
| PDPK1 | ENSG00000140992 | 0.00 | 0.00 | 0 | 0 |
| KLHL18 | ENSG00000114648 | 0.00 | 0.91 | 0 | 5 |
| DHRS12 | ENSG00000102796 | 0.00 | 0.50 | 0 | 3 |
| ABCA1 | ENSG00000165029 | 0.00 | 0.00 | 0 | 0 |
| CASP10 | ENSG00000003400 | 0.00 | 0.00 | 0 | 0 |
| TDRD5 | ENSG00000162782 | 0.00 | 0.00 | 0 | 0 |
| GGCX | ENSG00000115486 | 0.26 | 0.00 | 1 | 0 |
| FPR2 | ENSG00000171049 | 0.00 | 0.00 | 0 | 0 |
| PYGB | ENSG00000100994 | 0.00 | 0.00 | 0 | 0 |
| PREP | ENSG00000085377 | 0.00 | 0.82 | 0 | 5 |
| FGB | ENSG00000171564 | 0.00 | 0.00 | 0 | 0 |
| SLC26A11 | ENSG00000181045 | 1.27 | 0.00 | 5 | 0 |
| BMP3 | ENSG00000152785 | 0.00 | 0.00 | 0 | 0 |
| MTMR6 | ENSG00000139505 | 0.00 | 0.18 | 0 | 1 |
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