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 |
| CD6 | ENSG00000013725 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 | 0.06 | 0.02 | 0.06 | 0.02 | 0.12 | 0.03 | 0.13 | 0.03 | 0.04 | 0.03 | 0.01 | 0.01 | 0.05 | 0.02 | 0.00 | 0.02 | 0.04 | 0.02 | 0.04 | 0.09 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.13 | 0.07 | 0.11 | 0.05 | 0.05 | 0.03 | 0.04 | 0.02 | 0.14 | 0.14 | 0.06 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 |
| YAF2 | ENSG00000015153 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.03 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.03 | 0.06 | 0.02 | 0.02 | 0.04 | 0.03 | 0.06 | 0.10 | 0.04 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.03 | 0.18 | 0.03 | 0.03 | 0.00 | 0.05 | 0.01 | 0.10 | 0.05 | 0.15 | 0.09 | 0.06 | 0.02 | 0.00 | 0.01 | 0.05 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 | 0.00 | 0.00 | 0.05 | 0.06 |
| NPC1L1 | ENSG00000015520 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.09 | 0.02 | 0.03 | 0.01 | 0.11 | 0.02 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.10 | 0.06 | 0.01 | 0.00 | 0.04 | 0.01 | 0.10 | 0.00 | 0.07 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.11 | 0.02 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 |
| CLCA4 | ENSG00000016602 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.30 | 0.03 | 0.09 | 0.05 | 0.05 | 0.01 | 0.06 | 0.01 | 0.07 | 0.01 | 0.07 | 0.00 | 0.07 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.10 | 0.04 | 0.07 | 0.00 | 0.23 | 0.00 | 0.00 | 0.04 | 0.09 | 0.12 | 0.19 | 0.03 | 0.04 | 0.01 | 0.03 | 0.10 | 0.05 | 0.12 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.04 | 0.03 | 0.03 | 0.02 | 0.10 |
| SLC11A1 | ENSG00000018280 | 0.02 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.26 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.03 | 0.05 | 0.19 | 0.01 | 0.18 | 0.03 | 0.13 | 0.07 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.04 | 0.05 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.20 | 0.16 | 0.04 | 0.34 | 0.08 | 0.04 | 0.12 | 0.05 | 0.08 | 0.21 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 |
| ATP1A2 | ENSG00000018625 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.76 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.28 | 0.00 | 0.28 | 0.00 | 0.06 | 0.00 | 0.27 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.44 | 0.02 | 0.16 | 0.00 | 0.15 | 0.00 | 0.28 | 0.00 | 0.51 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.16 | 0.00 |
| VSIG2 | ENSG00000019102 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.02 | 0.02 | 0.06 | 0.03 | 0.09 | 0.00 | 0.00 | 0.11 | 0.06 | 0.05 | 0.09 | 0.04 | 0.11 | 0.04 | 0.14 | 0.04 | 0.16 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.19 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.22 | 0.19 | 0.17 | 0.04 | 0.31 | 0.04 | 0.07 | 0.05 | 0.17 | 0.06 | 0.23 | 0.00 | 0.24 | 0.03 | 0.00 | 0.13 | 0.02 | 0.07 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.01 | 0.26 |
| CYP24A1 | ENSG00000019186 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.11 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.23 | 0.02 | 0.06 | 0.02 | 0.01 | 0.02 | 0.14 | 0.01 | 0.30 | 0.01 | 0.14 | 0.00 | 0.09 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.45 | 0.01 | 0.35 | 0.03 | 0.04 | 0.02 | 0.10 | 0.01 | 0.22 | 0.00 | 0.16 | 0.03 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.00 |
| CD74 | ENSG00000019582 | 0.30 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 | 0.04 | 0.04 | 0.01 | 0.03 | 0.01 | 0.04 | 0.04 | 0.01 | 0.05 | 0.04 | 0.01 | 0.01 | 0.04 | 0.01 | 0.02 | 0.02 | 0.11 | 0.02 | 0.09 | 0.01 | 0.26 | 0.04 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.02 | 0.18 | 0.09 | 0.02 | 0.01 | 0.05 | 0.02 | 0.11 | 0.02 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.06 | 0.01 | 0.03 | 0.00 | 0.03 | 0.04 | 0.14 |
| SLC45A4 | ENSG00000022567 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.06 | 0.02 | 0.18 | 0.03 | 0.02 | 0.00 | 0.10 | 0.04 | 0.30 | 0.01 | 0.35 | 0.02 | 0.28 | 0.00 | 0.47 | 0.02 | 0.24 | 0.02 | 0.16 | 0.03 | 0.24 | 0.02 | 0.16 | 0.01 | 0.34 | 0.01 | 0.25 | 0.01 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.44 | 0.05 | 1.53 | 0.04 | 0.21 | 0.01 | 0.14 | 0.02 | 0.28 | 0.03 | 0.19 | 0.06 | 0.03 | 0.03 | 0.02 | 0.00 | 0.26 | 0.01 | 0.17 | 0.02 | 0.03 | 0.02 | 0.50 | 0.00 | 0.22 | 0.02 |
| RNASET2 | ENSG00000026297 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.06 | 0.03 | 0.11 | 0.00 | 0.01 | 0.02 | 0.09 | 0.02 | 0.06 | 0.08 | 0.07 | 0.05 | 0.05 | 0.12 | 0.05 | 0.10 | 0.09 | 0.02 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.01 | 0.14 | 0.00 | 0.18 | 0.10 | 0.08 | 0.00 | 0.04 | 0.01 | 0.01 | 0.07 | 0.13 | 0.07 | 0.45 | 0.00 | 0.10 | 0.03 | 0.05 | 0.20 | 0.06 | 0.21 | 0.08 | 0.01 | 0.05 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.05 | 0.00 | 0.14 | 0.00 | 0.06 | 0.04 | 0.16 |
| BTN3A1 | ENSG00000026950 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.21 | 0.03 | 0.00 | 0.01 | 0.02 | 0.05 | 0.08 | 0.01 | 0.07 | 0.06 | 0.02 | 0.04 | 0.11 | 0.10 | 0.06 | 0.05 | 0.03 | 0.02 | 0.04 | 0.03 | 0.02 | 0.04 | 0.10 | 0.01 | 0.06 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.35 | 0.05 | 0.09 | 0.03 | 0.04 | 0.01 | 0.20 | 0.02 | 0.03 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.11 | 0.00 | 0.13 | 0.01 |
| IBSP | ENSG00000029559 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.03 | 0.07 | 0.04 | 0.04 | 0.02 | 0.04 | 0.07 | 0.03 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.11 | 0.00 | 0.03 | 0.09 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.22 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.09 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 |
| BAK1 | ENSG00000030110 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.00 | 0.01 | 0.03 | 0.02 | 0.07 | 0.02 | 0.03 | 0.06 | 0.02 | 0.04 | 0.15 | 0.06 | 0.06 | 0.03 | 0.03 | 0.02 | 0.06 | 0.01 | 0.00 | 0.02 | 0.06 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.28 | 0.05 | 0.10 | 0.01 | 0.06 | 0.01 | 0.17 | 0.01 | 0.03 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.01 | 0.01 | 0.10 | 0.00 | 0.10 | 0.01 |
| MYOC | ENSG00000034971 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.43 | 0.01 | 0.02 | 0.00 | 0.10 | 0.03 | 0.12 | 0.01 | 0.23 | 0.01 | 0.04 | 0.00 | 0.19 | 0.01 | 0.12 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.05 | 0.00 | 0.23 | 0.01 | 0.22 | 0.00 | 0.00 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.19 | 0.01 | 0.36 | 0.02 | 0.14 | 0.00 | 0.11 | 0.00 | 0.34 | 0.00 | 0.78 | 0.03 | 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 | 0.00 |
| OTC | ENSG00000036473 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.03 | 0.02 | 0.01 | 0.03 | 0.09 | 0.05 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.13 | 0.00 | 0.01 | 0.03 | 0.03 | 0.11 | 0.07 | 0.19 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SLC18A1 | ENSG00000036565 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.21 | 0.00 | 0.14 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.06 | 0.01 | 0.08 | 0.02 | 0.07 | 0.05 | 0.06 | 0.06 | 0.04 | 0.00 | 0.12 | 0.00 | 0.17 | 0.00 | 0.05 | 0.00 | 0.13 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.15 | 0.02 | 0.41 | 0.01 | 0.05 | 0.00 | 0.09 | 0.07 | 0.24 | 0.01 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.01 | 0.01 | 0.05 |
| TUBG2 | ENSG00000037042 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.06 | 0.01 | 0.02 | 0.05 | 0.03 | 0.01 | 0.13 | 0.02 | 0.10 | 0.03 | 0.04 | 0.01 | 0.03 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.02 | 0.01 | 0.01 | 0.14 | 0.01 | 0.12 | 0.00 | 0.00 | 0.04 | 0.10 | 0.01 | 0.15 | 0.02 | 0.03 | 0.02 | 0.08 | 0.01 | 0.18 | 0.04 | 0.10 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 |
| PI4K2B | ENSG00000038210 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.05 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.01 | 0.06 | 0.04 | 0.04 | 0.05 | 0.06 | 0.01 | 0.02 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.10 | 0.07 | 0.00 | 0.02 | 0.02 | 0.04 | 0.06 | 0.07 | 0.14 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.05 | 0.01 |
| TLL1 | ENSG00000038295 | 0.00 | 0.02 | 0.00 | 0.02 | 0.06 | 0.02 | 0.03 | 0.02 | 0.04 | 0.13 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.08 | 0.02 | 0.14 | 0.03 | 0.09 | 0.08 | 0.06 | 0.05 | 0.11 | 0.02 | 0.07 | 0.02 | 0.06 | 0.00 | 0.04 | 0.06 | 0.10 | 0.00 | 0.15 | 0.10 | 0.07 | 0.00 | 0.07 | 0.00 | 0.00 | 0.05 | 0.07 | 0.08 | 0.29 | 0.05 | 0.08 | 0.03 | 0.05 | 0.09 | 0.05 | 0.08 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.10 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.06 |
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