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 |
| LIG1 | ENSG00000105486 | 0.18 | 0.55 | 1 | 2 |
| MSLN | ENSG00000102854 | 0.00 | 0.00 | 0 | 0 |
| ADAMTS12 | ENSG00000151388 | 0.00 | 0.00 | 0 | 0 |
| SLC6A13 | ENSG00000010379 | 1.04 | 0.00 | 2 | 0 |
| NRXN2 | ENSG00000110076 | 0.00 | 0.00 | 0 | 0 |
| PTPRA | ENSG00000132670 | 0.34 | 0.00 | 1 | 0 |
| LMAN1 | ENSG00000074695 | 0.00 | 0.32 | 0 | 3 |
| ABCC4 | ENSG00000125257 | 0.48 | 0.00 | 3 | 0 |
| SLC26A6 | ENSG00000225697 | 0.00 | 0.78 | 0 | 5 |
| MFSD4 | ENSG00000174514 | 0.00 | 0.00 | 0 | 0 |
| PMPCA | ENSG00000165688 | 0.00 | 0.36 | 0 | 2 |
| PXDN | ENSG00000130508 | 0.00 | 0.37 | 0 | 2 |
| ADAMTS3 | ENSG00000156140 | 0.36 | 0.00 | 1 | 0 |
| EPHX2 | ENSG00000120915 | 0.00 | 0.39 | 0 | 3 |
| PTPN22 | ENSG00000134242 | 0.00 | 0.30 | 0 | 2 |
| TEC | ENSG00000135605 | 0.00 | 0.00 | 0 | 0 |
| LRRK2 | ENSG00000188906 | 0.00 | 0.00 | 0 | 0 |
| TMIGD2 | ENSG00000167664 | 0.00 | 0.00 | 0 | 0 |
| PENK | ENSG00000181195 | 0.00 | 0.00 | 0 | 0 |
| ABCB7 | ENSG00000131269 | 0.00 | 0.00 | 0 | 0 |
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