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 |
| PHYKPL | ENSG00000175309 | 0.33 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.12 | 0.00 | 0.01 | 0.03 | 0.07 | 0.10 | 0.04 | 0.04 | 0.05 | 0.02 | 0.07 | 0.11 | 0.02 | 0.04 | 0.04 | 0.02 | 0.02 | 0.04 | 0.03 | 0.03 | 0.01 | 0.13 | 0.02 | 0.05 | 0.01 | 0.37 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.10 | 0.04 | 0.24 | 0.14 | 0.03 | 0.04 | 0.06 | 0.02 | 0.15 | 0.02 | 0.17 | 0.09 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.07 | 0.02 | 0.06 | 0.04 | 0.02 | 0.08 | 0.09 |
| CST6 | ENSG00000175315 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.09 | 0.00 | 0.17 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.09 | 0.01 | 0.10 | 0.01 | 0.31 | 0.01 | 0.18 | 0.01 | 0.07 | 0.03 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.09 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.15 | 0.05 | 0.22 | 0.03 | 0.13 | 0.00 | 0.05 | 0.02 | 0.26 | 0.06 | 0.12 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.05 |
| APOF | ENSG00000175336 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.01 | 0.04 | 0.01 | 0.02 | 0.02 | 0.08 | 0.04 | 0.06 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.25 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.23 | 0.04 | 0.04 | 0.02 | 0.08 | 0.00 | 0.45 | 0.04 | 0.12 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.05 | 0.04 | 0.00 | 0.00 | 0.07 | 0.03 |
| CHRNA7 | ENSG00000175344 | 0.01 | 0.00 | 0.01 | 0.03 | 0.14 | 0.00 | 0.01 | 0.05 | 0.03 | 0.10 | 0.00 | 0.00 | 0.01 | 0.29 | 0.02 | 0.12 | 0.05 | 0.10 | 0.03 | 0.04 | 0.10 | 0.06 | 0.02 | 0.07 | 0.02 | 0.07 | 0.01 | 0.06 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.07 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.13 | 0.07 | 0.32 | 0.04 | 0.05 | 0.02 | 0.08 | 0.07 | 0.48 | 0.10 | 0.09 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.01 | 0.11 | 0.02 | 0.00 | 0.03 | 0.15 |
| TMEM9B | ENSG00000175348 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.09 | 0.00 | 0.00 | 0.02 | 0.06 | 0.02 | 0.05 | 0.01 | 0.14 | 0.01 | 0.06 | 0.05 | 0.07 | 0.03 | 0.04 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.04 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.04 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.09 | 0.02 | 0.40 | 0.01 | 0.05 | 0.03 | 0.07 | 0.03 | 0.10 | 0.03 | 0.13 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.08 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.03 |
| OR10P1 | ENSG00000175398 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.08 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.06 | 0.03 | 0.09 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.18 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.18 | 0.04 | 0.03 | 0.00 | 0.07 | 0.01 | 0.12 | 0.09 | 0.25 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.04 | 0.05 | 0.00 | 0.00 | 0.05 | 0.03 |
| PCSK1 | ENSG00000175426 | 0.05 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.01 | 0.16 | 0.02 | 0.09 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.07 | 0.03 | 0.08 | 0.00 | 0.08 | 0.03 | 0.10 | 0.01 | 0.11 | 0.00 | 0.10 | 0.01 | 0.02 | 0.01 | 0.04 | 0.04 | 0.04 | 0.00 | 0.06 | 0.12 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.08 | 0.06 | 0.51 | 0.00 | 0.05 | 0.01 | 0.07 | 0.00 | 0.17 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.03 |
| LPL | ENSG00000175445 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.21 | 0.00 | 0.13 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.06 | 0.01 | 0.08 | 0.01 | 0.06 | 0.05 | 0.06 | 0.06 | 0.04 | 0.00 | 0.12 | 0.00 | 0.17 | 0.00 | 0.05 | 0.00 | 0.12 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.14 | 0.01 | 0.41 | 0.02 | 0.05 | 0.00 | 0.09 | 0.07 | 0.24 | 0.06 | 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 |
| OR52W1 | ENSG00000175485 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.10 | 0.00 | 0.00 | 0.02 | 0.08 | 0.01 | 0.06 | 0.02 | 0.14 | 0.01 | 0.06 | 0.06 | 0.09 | 0.04 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.10 | 0.01 | 0.42 | 0.01 | 0.05 | 0.02 | 0.07 | 0.03 | 0.09 | 0.04 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.09 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.03 |
| CLCF1 | ENSG00000175505 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.11 | 0.00 | 0.23 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.15 | 0.01 | 0.19 | 0.01 | 0.44 | 0.01 | 0.40 | 0.02 | 0.18 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 | 0.02 | 0.01 | 0.16 | 0.01 | 0.20 | 0.02 | 0.08 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.49 | 0.03 | 0.28 | 0.03 | 0.21 | 0.00 | 0.18 | 0.02 | 0.29 | 0.02 | 0.13 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.18 | 0.02 |
| GPR152 | ENSG00000175514 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.10 | 0.00 | 0.21 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.15 | 0.01 | 0.18 | 0.02 | 0.42 | 0.01 | 0.40 | 0.02 | 0.16 | 0.03 | 0.01 | 0.01 | 0.05 | 0.02 | 0.02 | 0.01 | 0.14 | 0.01 | 0.20 | 0.02 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.49 | 0.03 | 0.29 | 0.03 | 0.24 | 0.01 | 0.17 | 0.02 | 0.29 | 0.02 | 0.13 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.19 | 0.02 |
| PNLIP | ENSG00000175535 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.10 | 0.00 | 0.02 | 0.01 | 0.17 | 0.03 | 0.02 | 0.04 | 0.05 | 0.01 | 0.03 | 0.04 | 0.06 | 0.07 | 0.05 | 0.01 | 0.06 | 0.01 | 0.05 | 0.01 | 0.01 | 0.02 | 0.10 | 0.14 | 0.25 | 0.12 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.09 | 0.14 | 0.22 | 0.01 | 0.06 | 0.05 | 0.06 | 0.04 | 0.05 | 0.04 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.12 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 |
| UCP3 | ENSG00000175564 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.05 | 0.01 | 0.19 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.14 | 0.02 | 0.20 | 0.02 | 0.27 | 0.03 | 0.49 | 0.03 | 0.12 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.03 | 0.08 | 0.02 | 0.07 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.34 | 0.06 | 0.49 | 0.03 | 0.11 | 0.01 | 0.11 | 0.01 | 0.13 | 0.10 | 0.16 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.28 | 0.01 |
| UCP2 | ENSG00000175567 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.05 | 0.01 | 0.19 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.14 | 0.02 | 0.20 | 0.02 | 0.27 | 0.03 | 0.51 | 0.03 | 0.12 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.03 | 0.08 | 0.02 | 0.07 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.34 | 0.06 | 0.49 | 0.03 | 0.11 | 0.01 | 0.10 | 0.01 | 0.13 | 0.10 | 0.16 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.28 | 0.02 |
| OR4B1 | ENSG00000175619 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.06 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 | 0.03 | 0.05 | 0.01 | 0.07 | 0.04 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.07 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.09 | 0.06 | 0.05 | 0.03 | 0.03 | 0.02 | 0.05 | 0.07 | 0.09 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.04 |
| DRD5P2 | ENSG00000175658 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.09 | 0.02 | 0.07 | 0.02 | 0.10 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.11 | 0.05 | 0.04 | 0.01 | 0.05 | 0.02 | 0.08 | 0.02 | 0.20 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| NR2F1 | ENSG00000175745 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.15 | 0.02 | 0.08 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.01 | 0.09 | 0.01 | 0.07 | 0.02 | 0.13 | 0.01 | 0.12 | 0.01 | 0.11 | 0.01 | 0.02 | 0.01 | 0.06 | 0.02 | 0.04 | 0.00 | 0.07 | 0.18 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.07 | 0.05 | 0.54 | 0.01 | 0.05 | 0.01 | 0.08 | 0.03 | 0.17 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 |
| AURKAIP1 | ENSG00000175756 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.09 | 0.06 | 0.08 | 0.11 | 0.06 | 0.09 | 0.13 | 0.08 | 0.09 | 0.09 | 0.02 | 0.11 | 0.00 | 0.17 | 0.05 | 0.05 | 0.02 | 0.31 | 0.00 | 1.01 | 0.05 | 0.17 | 0.01 | 0.12 | 0.00 | 0.00 | 0.04 | 0.19 | 0.23 | 0.38 | 0.06 | 0.11 | 0.05 | 0.12 | 0.08 | 0.27 | 0.18 | 0.28 | 0.10 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.00 | 0.03 | 0.03 | 0.15 | 0.00 | 0.14 | 0.07 | 0.13 |
| SLC35E3 | ENSG00000175782 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.57 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.34 | 0.01 | 0.25 | 0.01 | 0.25 | 0.02 | 0.36 | 0.01 | 0.40 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 | 0.11 | 0.01 | 0.09 | 0.00 | 0.26 | 0.01 | 0.33 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.29 | 0.02 | 0.27 | 0.04 | 0.09 | 0.01 | 0.03 | 0.01 | 0.46 | 0.07 | 1.75 | 0.04 | 0.26 | 0.00 | 0.00 | 0.01 | 0.12 | 0.00 | 0.06 | 0.02 | 0.69 | 0.02 | 0.00 | 0.00 | 0.32 | 0.01 |
| PRIMA1 | ENSG00000175785 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.06 | 0.11 | 0.02 | 0.05 | 0.04 | 0.06 | 0.06 | 0.04 | 0.04 | 0.00 | 0.04 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.10 | 0.00 | 0.31 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.20 | 0.17 | 0.07 | 0.09 | 0.05 | 0.03 | 0.06 | 0.02 | 0.06 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.11 | 0.01 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
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