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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| KIRC | KIRP | KICH | PRAD | BLCA | THYM | MESO | LUAD | LUSC | HNSC | ESCA | STAD | COAD | READ | PAAD | LIHC | CHOL | ACC | PCPG | THCA | BRCA | OV | CESC | UCEC | UCS | SARC | TGCT | LAML | DLBC | LGG | GBM | UVM | SKCM | |||||||||||||||||||||||||||||||||||
| HGNC Symbol | Ensembl Gene ID | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del |
| NUAK1 | ENSG00000074590 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.09 | 0.03 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.05 | 0.03 | 0.04 | 0.02 | 0.03 | 0.05 | 0.05 | 0.06 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.06 | 0.05 | 0.04 | 0.00 | 0.22 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.07 | 0.08 | 0.23 | 0.02 | 0.01 | 0.03 | 0.05 | 0.06 | 0.11 | 0.17 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 |
| TNFSF13B | ENSG00000102524 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.20 | 0.02 | 0.00 | 0.01 | 0.03 | 0.00 | 0.14 | 0.04 | 0.15 | 0.04 | 0.11 | 0.01 | 0.17 | 0.04 | 0.14 | 0.03 | 0.10 | 0.01 | 0.16 | 0.01 | 0.02 | 0.01 | 0.25 | 0.00 | 0.17 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.04 | 0.26 | 0.10 | 0.20 | 0.01 | 0.07 | 0.01 | 0.33 | 0.09 | 0.28 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.12 | 0.06 | 0.02 | 0.07 | 0.02 | 0.05 | 0.00 | 0.06 | 0.07 |
| PNCK | ENSG00000130822 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.22 | 0.01 | 0.18 | 0.02 | 0.14 | 0.01 | 0.24 | 0.01 | 0.18 | 0.02 | 0.05 | 0.00 | 0.10 | 0.01 | 0.07 | 0.00 | 0.12 | 0.03 | 0.10 | 0.01 | 0.16 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.44 | 0.09 | 0.22 | 0.02 | 0.12 | 0.03 | 0.17 | 0.07 | 0.24 | 0.07 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.03 | 0.02 | 0.05 | 0.00 | 0.06 | 0.01 |
| HHIPL1 | ENSG00000182218 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.04 | 0.01 | 0.04 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.04 | 0.06 | 0.18 | 0.02 | 0.07 | 0.05 | 0.08 | 0.04 | 0.03 | 0.06 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.10 | 0.00 | 0.31 | 0.11 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.07 | 0.22 | 0.16 | 0.06 | 0.10 | 0.05 | 0.02 | 0.20 | 0.05 | 0.14 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| RHCG | ENSG00000140519 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.03 | 0.03 | 0.00 | 0.06 | 0.00 | 0.05 | 0.01 | 0.22 | 0.00 | 0.06 | 0.02 | 0.19 | 0.01 | 0.25 | 0.00 | 0.04 | 0.01 | 0.10 | 0.00 | 0.06 | 0.00 | 0.05 | 0.04 | 0.05 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.03 | 0.31 | 0.07 | 0.18 | 0.00 | 0.04 | 0.02 | 0.22 | 0.05 | 0.12 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.20 | 0.01 |
| PDE7A | ENSG00000205268 | 0.00 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.04 | 0.02 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.15 | 0.02 | 0.10 | 0.03 | 0.06 | 0.01 | 0.10 | 0.01 | 0.10 | 0.02 | 0.06 | 0.00 | 0.16 | 0.03 | 0.01 | 0.02 | 0.07 | 0.01 | 0.06 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.20 | 0.02 | 0.32 | 0.07 | 0.03 | 0.01 | 0.08 | 0.01 | 0.26 | 0.10 | 0.13 | 0.04 | 0.20 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.01 | 0.22 | 0.00 | 0.07 | 0.01 |
| RXFP1 | ENSG00000171509 | 0.01 | 0.02 | 0.00 | 0.02 | 0.06 | 0.02 | 0.03 | 0.04 | 0.05 | 0.13 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.06 | 0.02 | 0.13 | 0.02 | 0.10 | 0.16 | 0.11 | 0.07 | 0.08 | 0.01 | 0.07 | 0.02 | 0.04 | 0.00 | 0.03 | 0.06 | 0.07 | 0.06 | 0.11 | 0.10 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.08 | 0.06 | 0.30 | 0.04 | 0.08 | 0.03 | 0.05 | 0.12 | 0.05 | 0.12 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.08 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.06 |
| GBA | ENSG00000177628 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.08 | 0.01 | 0.35 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.37 | 0.00 | 0.26 | 0.00 | 0.05 | 0.00 | 0.20 | 0.00 | 0.16 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.39 | 0.00 | 0.65 | 0.01 | 0.18 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.34 | 0.00 | 0.58 | 0.02 | 0.19 | 0.00 | 0.24 | 0.00 | 0.93 | 0.01 | 0.35 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.19 | 0.00 |
| SLC18B1 | ENSG00000146409 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.00 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.14 | 0.03 | 0.04 | 0.05 | 0.03 | 0.06 | 0.02 | 0.11 | 0.02 | 0.09 | 0.02 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.01 | 0.08 | 0.00 | 0.10 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.05 | 0.06 | 0.28 | 0.01 | 0.02 | 0.05 | 0.03 | 0.08 | 0.03 | 0.29 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.05 | 0.00 | 0.10 | 0.01 | 0.06 | 0.01 | 0.13 |
| SEMA3D | ENSG00000153993 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.02 | 0.02 | 0.00 | 0.03 | 0.02 | 0.05 | 0.01 | 0.22 | 0.02 | 0.12 | 0.01 | 0.31 | 0.03 | 0.16 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.06 | 0.02 | 0.04 | 0.01 | 0.05 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.03 | 0.19 | 0.06 | 0.05 | 0.01 | 0.02 | 0.02 | 0.07 | 0.05 | 0.09 | 0.05 | 0.10 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 |
| PTPN4 | ENSG00000088179 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.05 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.07 | 0.01 | 0.13 | 0.01 | 0.12 | 0.01 | 0.31 | 0.03 | 0.05 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.10 | 0.14 | 0.03 | 0.00 | 0.06 | 0.02 | 0.18 | 0.00 | 0.16 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SP140 | ENSG00000079263 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.31 | 0.00 | 0.03 | 0.00 | 0.07 | 0.03 | 0.04 | 0.02 | 0.20 | 0.01 | 0.18 | 0.04 | 0.15 | 0.04 | 0.04 | 0.02 | 0.03 | 0.02 | 0.02 | 0.07 | 0.01 | 0.03 | 0.05 | 0.00 | 0.04 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.09 | 0.14 | 0.20 | 0.01 | 0.36 | 0.03 | 0.05 | 0.13 | 0.06 | 0.04 | 0.34 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.04 | 0.05 | 0.02 | 0.08 |
| COL12A1 | ENSG00000111799 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.16 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.05 | 0.04 | 0.05 | 0.07 | 0.03 | 0.03 | 0.03 | 0.05 | 0.07 | 0.05 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.22 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.08 | 0.15 | 0.10 | 0.02 | 0.02 | 0.07 | 0.01 | 0.09 | 0.11 | 0.04 | 0.16 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.00 | 0.01 | 0.00 | 0.04 | 0.05 | 0.05 | 0.02 | 0.04 |
| PAK2 | ENSG00000180370 | 0.05 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.07 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.14 | 0.07 | 1.39 | 0.01 | 0.58 | 0.00 | 0.77 | 0.03 | 0.22 | 0.03 | 0.06 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.13 | 0.03 | 0.12 | 0.03 | 0.10 | 0.09 | 0.00 | 0.10 | 0.00 | 0.00 | 0.21 | 0.03 | 1.00 | 0.09 | 0.65 | 0.00 | 0.37 | 0.01 | 0.77 | 0.18 | 0.08 | 0.12 | 0.11 | 0.04 | 0.00 | 0.00 | 0.35 | 0.01 | 0.03 | 0.07 | 0.07 | 0.08 | 0.00 | 0.00 | 0.03 | 0.03 |
| FMO1 | ENSG00000010932 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.41 | 0.01 | 0.02 | 0.00 | 0.10 | 0.03 | 0.12 | 0.01 | 0.23 | 0.01 | 0.04 | 0.00 | 0.20 | 0.01 | 0.12 | 0.01 | 0.03 | 0.00 | 0.12 | 0.00 | 0.06 | 0.00 | 0.21 | 0.01 | 0.22 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.18 | 0.02 | 0.34 | 0.02 | 0.13 | 0.00 | 0.10 | 0.00 | 0.29 | 0.00 | 0.61 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.30 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.14 | 0.01 |
| RIPK2 | ENSG00000104312 | 0.00 | 0.01 | 0.01 | 0.00 | 0.06 | 0.00 | 0.08 | 0.02 | 0.22 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.13 | 0.02 | 0.14 | 0.03 | 0.08 | 0.00 | 0.18 | 0.03 | 0.14 | 0.01 | 0.10 | 0.02 | 0.16 | 0.02 | 0.03 | 0.01 | 0.15 | 0.01 | 0.20 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.34 | 0.01 | 0.31 | 0.10 | 0.06 | 0.01 | 0.08 | 0.01 | 0.35 | 0.05 | 0.18 | 0.06 | 0.15 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.04 | 0.01 | 0.01 | 0.01 | 0.33 | 0.00 | 0.09 | 0.01 |
| TIE1 | ENSG00000066056 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.14 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.11 | 0.02 | 0.11 | 0.01 | 0.08 | 0.02 | 0.12 | 0.01 | 0.05 | 0.02 | 0.03 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.06 | 0.09 | 0.00 | 0.22 | 0.01 | 0.03 | 0.02 | 0.09 | 0.00 | 0.00 | 0.08 | 0.04 | 0.59 | 0.05 | 0.10 | 0.00 | 0.11 | 0.02 | 0.18 | 0.05 | 0.12 | 0.04 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.05 | 0.02 |
| BRWD1 | ENSG00000185658 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.29 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.03 | 0.06 | 0.02 | 0.05 | 0.02 | 0.09 | 0.03 | 0.07 | 0.01 | 0.02 | 0.00 | 0.08 | 0.01 | 0.01 | 0.02 | 0.01 | 0.07 | 0.03 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.14 | 0.12 | 0.09 | 0.02 | 0.04 | 0.01 | 0.04 | 0.03 | 0.07 | 0.07 | 0.04 | 0.00 | 0.15 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 |
| CRISP3 | ENSG00000096006 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.01 | 0.20 | 0.04 | 0.05 | 0.03 | 0.32 | 0.02 | 0.14 | 0.02 | 0.03 | 0.01 | 0.12 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.22 | 0.06 | 0.08 | 0.04 | 0.04 | 0.01 | 0.20 | 0.03 | 0.08 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.02 |
| SLC1A3 | ENSG00000079215 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.15 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.22 | 0.01 | 0.23 | 0.00 | 0.08 | 0.00 | 0.10 | 0.01 | 0.19 | 0.02 | 0.05 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.23 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.25 | 0.02 | 0.07 | 0.00 | 0.11 | 0.01 | 0.50 | 0.03 | 0.26 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.14 | 0.01 |
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