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 |
| LRRK1 | ENSG00000154237 | 1.54 | 0.00 | 6 | 0 |
| MLYCD | ENSG00000103150 | 0.00 | 0.17 | 0 | 1 |
| KCNQ2 | ENSG00000075043 | 0.19 | 0.00 | 1 | 0 |
| ST3GAL2 | ENSG00000157350 | 0.28 | 0.12 | 2 | 1 |
| ITGB7 | ENSG00000139626 | 0.00 | 0.00 | 0 | 0 |
| KLHL4 | ENSG00000102271 | 0.00 | 0.00 | 0 | 0 |
| ALPL | ENSG00000162551 | 0.00 | 1.59 | 0 | 4 |
| MFSD2A | ENSG00000168389 | 0.82 | 0.00 | 3 | 0 |
| PLCG2 | ENSG00000197943 | 0.00 | 0.00 | 0 | 0 |
| SGK2 | ENSG00000101049 | 0.12 | 0.00 | 1 | 0 |
| RAPGEF4 | ENSG00000091428 | 0.00 | 0.00 | 0 | 0 |
| SPINT1 | ENSG00000166145 | 0.00 | 0.39 | 0 | 3 |
| UGT8 | ENSG00000174607 | 0.00 | 0.00 | 0 | 0 |
| RABGGTA | ENSG00000100949 | 0.00 | 0.00 | 0 | 0 |
| SEMA7A | ENSG00000138623 | 0.00 | 0.00 | 0 | 0 |
| SLC4A4 | ENSG00000080493 | 0.00 | 0.00 | 0 | 0 |
| ADAMTS1 | ENSG00000154734 | 0.00 | 0.00 | 0 | 0 |
| CASP14 | ENSG00000105141 | 0.00 | 0.00 | 0 | 0 |
| CD96 | ENSG00000153283 | 0.00 | 0.00 | 0 | 0 |
| PARP1 | ENSG00000143799 | 0.00 | 0.23 | 0 | 1 |
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