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 |
| PTK2 | ENSG00000169398 | 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 | 0.28 | 0.01 | 0.34 | 0.02 | 0.28 | 0.00 | 0.48 | 0.02 | 0.22 | 0.03 | 0.16 | 0.03 | 0.25 | 0.03 | 0.16 | 0.02 | 0.34 | 0.01 | 0.25 | 0.01 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.44 | 0.05 | 1.52 | 0.06 | 0.21 | 0.02 | 0.12 | 0.03 | 0.28 | 0.03 | 0.19 | 0.08 | 0.03 | 0.03 | 0.02 | 0.00 | 0.26 | 0.01 | 0.17 | 0.02 | 0.03 | 0.02 | 0.50 | 0.00 | 0.23 | 0.02 |
| SCD | ENSG00000099194 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.10 | 0.02 | 0.11 | 0.00 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.03 | 0.07 | 0.00 | 0.06 | 0.02 | 0.08 | 0.02 | 0.09 | 0.00 | 0.10 | 0.00 | 0.07 | 0.01 | 0.03 | 0.03 | 0.06 | 0.11 | 0.14 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.06 | 0.34 | 0.01 | 0.07 | 0.02 | 0.09 | 0.05 | 0.09 | 0.03 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 |
| DCLK2 | ENSG00000170390 | 0.01 | 0.02 | 0.00 | 0.02 | 0.06 | 0.00 | 0.02 | 0.01 | 0.08 | 0.12 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.04 | 0.01 | 0.11 | 0.02 | 0.07 | 0.08 | 0.07 | 0.06 | 0.06 | 0.02 | 0.03 | 0.02 | 0.02 | 0.00 | 0.03 | 0.06 | 0.05 | 0.00 | 0.12 | 0.10 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.05 | 0.10 | 0.24 | 0.03 | 0.07 | 0.04 | 0.05 | 0.18 | 0.04 | 0.12 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.08 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.05 |
| FDPS | ENSG00000160752 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.01 | 0.36 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.37 | 0.00 | 0.26 | 0.00 | 0.05 | 0.01 | 0.20 | 0.00 | 0.16 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.38 | 0.00 | 0.58 | 0.01 | 0.18 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.34 | 0.00 | 0.58 | 0.02 | 0.19 | 0.00 | 0.24 | 0.00 | 1.03 | 0.01 | 0.34 | 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 |
| ENPP3 | ENSG00000154269 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.17 | 0.03 | 0.04 | 0.06 | 0.03 | 0.04 | 0.02 | 0.11 | 0.03 | 0.06 | 0.04 | 0.02 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.02 | 0.09 | 0.00 | 0.16 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.12 | 0.05 | 0.08 | 0.27 | 0.01 | 0.02 | 0.06 | 0.03 | 0.08 | 0.03 | 0.27 | 0.06 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.05 | 0.00 | 0.11 | 0.00 | 0.05 | 0.01 | 0.12 |
| ERN1 | ENSG00000178607 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.25 | 0.01 | 0.03 | 0.00 | 0.12 | 0.00 | 0.14 | 0.01 | 0.19 | 0.01 | 0.07 | 0.02 | 0.21 | 0.02 | 0.11 | 0.02 | 0.07 | 0.01 | 0.07 | 0.02 | 0.07 | 0.10 | 0.21 | 0.00 | 0.12 | 0.01 | 0.21 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.58 | 0.01 | 0.24 | 0.03 | 0.17 | 0.02 | 0.10 | 0.03 | 0.36 | 0.02 | 0.17 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.24 | 0.01 |
| ABCA5 | ENSG00000154265 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.22 | 0.00 | 0.02 | 0.00 | 0.13 | 0.00 | 0.17 | 0.00 | 0.20 | 0.01 | 0.07 | 0.02 | 0.23 | 0.03 | 0.13 | 0.03 | 0.05 | 0.01 | 0.07 | 0.03 | 0.05 | 0.10 | 0.22 | 0.01 | 0.12 | 0.01 | 0.16 | 0.12 | 0.02 | 0.01 | 0.00 | 0.00 | 0.43 | 0.02 | 0.27 | 0.03 | 0.14 | 0.03 | 0.10 | 0.01 | 0.34 | 0.02 | 0.21 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.02 | 0.01 | 0.17 | 0.01 | 0.22 | 0.02 |
| CRTAC1 | ENSG00000095713 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.11 | 0.01 | 0.09 | 0.00 | 0.02 | 0.00 | 0.18 | 0.01 | 0.03 | 0.03 | 0.08 | 0.00 | 0.05 | 0.02 | 0.09 | 0.01 | 0.09 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.03 | 0.03 | 0.06 | 0.16 | 0.14 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.08 | 0.07 | 0.33 | 0.01 | 0.07 | 0.02 | 0.09 | 0.03 | 0.09 | 0.02 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 |
| FARS2 | ENSG00000145982 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.24 | 0.09 | 0.01 | 0.05 | 0.02 | 0.01 | 0.10 | 0.02 | 0.10 | 0.08 | 0.05 | 0.06 | 0.07 | 0.29 | 0.04 | 0.12 | 0.03 | 0.03 | 0.02 | 0.05 | 0.00 | 0.07 | 0.15 | 0.02 | 0.06 | 0.06 | 0.03 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.12 | 0.07 | 0.46 | 0.10 | 0.11 | 0.06 | 0.09 | 0.03 | 0.23 | 0.05 | 0.09 | 0.14 | 0.04 | 0.03 | 0.00 | 0.00 | 0.10 | 0.05 | 0.02 | 0.03 | 0.02 | 0.03 | 0.28 | 0.00 | 0.25 | 0.00 |
| ELP3 | ENSG00000134014 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.16 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.08 | 0.01 | 0.03 | 0.08 | 0.09 | 0.02 | 0.04 | 0.02 | 0.08 | 0.00 | 0.18 | 0.00 | 0.04 | 0.01 | 0.10 | 0.00 | 0.08 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.13 | 0.02 | 0.35 | 0.00 | 0.02 | 0.01 | 0.09 | 0.09 | 0.14 | 0.06 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.05 |
| AQP7 | ENSG00000165269 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.01 | 0.10 | 0.07 | 0.01 | 0.36 | 0.04 | 0.14 | 0.03 | 0.22 | 0.02 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.24 | 0.01 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.11 | 0.07 | 0.01 | 0.01 | 0.05 | 0.01 | 0.03 | 0.05 | 0.09 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.00 | 0.00 | 0.05 | 0.04 |
| CDK7 | ENSG00000134058 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.21 | 0.01 | 0.15 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.08 | 0.01 | 0.09 | 0.01 | 0.07 | 0.01 | 0.16 | 0.01 | 0.14 | 0.01 | 0.07 | 0.00 | 0.09 | 0.00 | 0.07 | 0.01 | 0.04 | 0.00 | 0.13 | 0.07 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.01 | 0.72 | 0.00 | 0.07 | 0.01 | 0.11 | 0.00 | 0.35 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| KMT2A | ENSG00000118058 | 0.02 | 0.01 | 0.00 | 0.06 | 0.02 | 0.02 | 0.02 | 0.08 | 0.04 | 0.11 | 0.00 | 0.02 | 0.09 | 0.04 | 0.06 | 0.08 | 0.05 | 0.09 | 0.05 | 0.16 | 0.04 | 0.12 | 0.09 | 0.07 | 0.01 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.01 | 0.09 | 0.00 | 0.17 | 0.07 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.22 | 0.18 | 0.14 | 0.04 | 0.30 | 0.06 | 0.04 | 0.32 | 0.16 | 0.03 | 0.23 | 0.00 | 0.15 | 0.19 | 0.03 | 0.14 | 0.01 | 0.07 | 0.01 | 0.03 | 0.01 | 0.00 | 0.07 | 0.00 | 0.26 |
| MTOR | ENSG00000198793 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.06 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.26 | 0.07 | 0.06 | 0.05 | 0.11 | 0.05 | 0.08 | 0.14 | 0.08 | 0.13 | 0.08 | 0.01 | 0.12 | 0.00 | 0.21 | 0.03 | 0.06 | 0.03 | 0.26 | 0.00 | 1.07 | 0.03 | 0.21 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.19 | 0.21 | 0.36 | 0.04 | 0.10 | 0.09 | 0.10 | 0.04 | 0.27 | 0.18 | 0.20 | 0.08 | 0.09 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.04 | 0.07 | 0.13 | 0.00 | 0.07 | 0.06 | 0.11 |
| COL7A1 | ENSG00000114270 | 0.00 | 0.18 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.03 | 0.03 | 0.14 | 0.00 | 0.03 | 0.00 | 0.55 | 0.01 | 0.07 | 0.00 | 0.10 | 0.00 | 0.06 | 0.03 | 0.11 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.10 | 0.00 | 0.04 | 0.03 | 0.05 | 0.00 | 0.24 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.16 | 0.11 | 0.20 | 0.01 | 0.06 | 0.07 | 0.05 | 0.15 | 0.32 | 0.03 | 0.13 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.11 | 0.01 | 0.06 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 |
| CLK2 | ENSG00000176444 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.08 | 0.01 | 0.35 | 0.02 | 0.02 | 0.00 | 0.11 | 0.00 | 0.37 | 0.00 | 0.27 | 0.00 | 0.05 | 0.01 | 0.20 | 0.00 | 0.16 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.37 | 0.00 | 0.65 | 0.01 | 0.18 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.34 | 0.00 | 0.58 | 0.02 | 0.19 | 0.00 | 0.24 | 0.00 | 1.03 | 0.01 | 0.37 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.19 | 0.00 |
| ATP6V0A4 | ENSG00000105929 | 0.01 | 0.01 | 0.09 | 0.00 | 0.06 | 0.00 | 0.02 | 0.02 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.05 | 0.08 | 0.02 | 0.08 | 0.06 | 0.03 | 0.14 | 0.04 | 0.19 | 0.03 | 0.07 | 0.03 | 0.00 | 0.03 | 0.01 | 0.01 | 0.05 | 0.05 | 0.04 | 0.00 | 0.02 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.04 | 0.49 | 0.04 | 0.04 | 0.08 | 0.06 | 0.05 | 0.16 | 0.14 | 0.11 | 0.08 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.11 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.22 | 0.02 |
| DUSP15 | ENSG00000149599 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.31 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.10 | 0.01 | 0.28 | 0.00 | 0.16 | 0.00 | 0.08 | 0.00 | 0.06 | 0.00 | 0.17 | 0.00 | 0.22 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.28 | 0.02 | 0.23 | 0.00 | 0.17 | 0.00 | 1.27 | 0.00 | 0.11 | 0.02 | 0.13 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 |
| SLC45A2 | ENSG00000164175 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.18 | 0.00 | 0.20 | 0.00 | 0.06 | 0.00 | 0.10 | 0.01 | 0.10 | 0.02 | 0.05 | 0.01 | 0.04 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.20 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.22 | 0.02 | 0.06 | 0.00 | 0.07 | 0.01 | 0.16 | 0.05 | 0.19 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.02 |
| PDCD1LG2 | ENSG00000197646 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.18 | 0.12 | 0.01 | 0.01 | 0.04 | 0.07 | 0.06 | 0.12 | 0.20 | 0.10 | 0.27 | 0.06 | 0.15 | 0.13 | 0.17 | 0.10 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.08 | 0.06 | 0.03 | 0.03 | 0.01 | 0.12 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.06 | 0.17 | 0.19 | 0.24 | 0.03 | 0.07 | 0.02 | 0.02 | 0.12 | 0.23 | 0.11 | 0.01 | 0.09 | 0.00 | 0.00 | 0.07 | 0.05 | 0.00 | 0.09 | 0.01 | 0.19 | 0.00 | 0.00 | 0.09 | 0.11 |
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