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 |
| EPHB3 | ENSG00000182580 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.17 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.15 | 0.05 | 1.85 | 0.00 | 0.63 | 0.00 | 0.76 | 0.01 | 0.27 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.04 | 0.01 | 0.11 | 0.02 | 0.12 | 0.01 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.20 | 0.02 | 1.14 | 0.02 | 0.62 | 0.00 | 0.33 | 0.01 | 0.80 | 0.09 | 0.13 | 0.10 | 0.22 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.05 | 0.00 | 0.19 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 |
| ADCY2 | ENSG00000078295 | 0.01 | 0.00 | 0.02 | 0.01 | 0.06 | 0.05 | 0.02 | 0.03 | 0.21 | 0.02 | 0.00 | 0.01 | 0.06 | 0.01 | 0.29 | 0.01 | 0.31 | 0.01 | 0.09 | 0.02 | 0.19 | 0.02 | 0.09 | 0.03 | 0.02 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.09 | 0.02 | 0.00 | 0.05 | 0.20 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.36 | 0.04 | 0.16 | 0.01 | 0.09 | 0.01 | 0.08 | 0.03 | 0.19 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.03 | 0.00 | 0.02 | 0.18 | 0.09 |
| ARID4B | ENSG00000054267 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.14 | 0.03 | 0.02 | 0.00 | 0.05 | 0.03 | 0.08 | 0.01 | 0.13 | 0.02 | 0.07 | 0.00 | 0.29 | 0.03 | 0.23 | 0.01 | 0.03 | 0.03 | 0.07 | 0.05 | 0.01 | 0.01 | 0.17 | 0.01 | 0.23 | 0.02 | 0.06 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.29 | 0.02 | 0.55 | 0.08 | 0.09 | 0.02 | 0.13 | 0.02 | 0.39 | 0.00 | 0.03 | 0.24 | 0.04 | 0.02 | 0.02 | 0.00 | 0.02 | 0.15 | 0.00 | 0.03 | 0.04 | 0.03 | 0.08 | 0.03 | 0.16 | 0.03 |
| PYGO2 | ENSG00000163348 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.38 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.38 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.21 | 0.00 | 0.17 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.40 | 0.00 | 0.53 | 0.01 | 0.21 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.35 | 0.00 | 0.52 | 0.02 | 0.21 | 0.00 | 0.18 | 0.00 | 0.60 | 0.00 | 0.36 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.02 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.21 | 0.01 |
| PLP1 | ENSG00000123560 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.11 | 0.01 | 0.03 | 0.01 | 0.08 | 0.02 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.05 | 0.04 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.17 | 0.10 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 |
| EMILIN3 | ENSG00000183798 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.04 | 0.08 | 0.01 | 0.01 | 0.02 | 0.04 | 0.01 | 0.09 | 0.00 | 0.09 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.08 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.05 | 0.09 | 0.02 | 0.02 | 0.05 | 0.01 | 0.28 | 0.04 | 0.17 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 |
| PTPRC | ENSG00000081237 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.11 | 0.05 | 0.02 | 0.00 | 0.10 | 0.00 | 0.11 | 0.01 | 0.08 | 0.03 | 0.05 | 0.01 | 0.13 | 0.06 | 0.05 | 0.01 | 0.03 | 0.01 | 0.11 | 0.03 | 0.01 | 0.00 | 0.22 | 0.01 | 0.20 | 0.02 | 0.06 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.20 | 0.01 | 0.28 | 0.06 | 0.07 | 0.00 | 0.07 | 0.01 | 0.07 | 0.03 | 0.09 | 0.11 | 0.07 | 0.00 | 0.01 | 0.01 | 0.26 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.06 | 0.00 | 0.18 | 0.02 |
| SLC25A24 | ENSG00000085491 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.34 | 0.01 | 0.13 | 0.01 | 0.13 | 0.01 | 0.12 | 0.03 | 0.12 | 0.03 | 0.06 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.05 | 0.10 | 0.12 | 0.15 | 0.02 | 0.08 | 0.02 | 0.03 | 0.01 | 0.06 | 0.05 | 0.10 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.08 | 0.10 |
| ADGRA2 | ENSG00000020181 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.07 | 0.49 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 | 0.17 | 0.03 | 0.85 | 0.04 | 0.26 | 0.03 | 0.39 | 0.06 | 0.09 | 0.03 | 0.11 | 0.04 | 0.09 | 0.04 | 0.09 | 0.01 | 0.05 | 0.06 | 0.02 | 0.02 | 0.16 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.80 | 0.04 | 0.22 | 0.10 | 0.05 | 0.02 | 0.10 | 0.05 | 0.52 | 0.11 | 0.15 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.03 |
| QSOX2 | ENSG00000165661 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.07 | 0.02 | 0.08 | 0.04 | 0.16 | 0.01 | 0.13 | 0.02 | 0.03 | 0.01 | 0.08 | 0.05 | 0.01 | 0.00 | 0.06 | 0.06 | 0.06 | 0.01 | 0.19 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.16 | 0.22 | 0.06 | 0.02 | 0.05 | 0.04 | 0.03 | 0.14 | 0.07 | 0.15 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.03 | 0.03 |
| SHPRH | ENSG00000146414 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.19 | 0.02 | 0.06 | 0.06 | 0.03 | 0.03 | 0.03 | 0.12 | 0.03 | 0.09 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.03 | 0.01 | 0.10 | 0.00 | 0.18 | 0.18 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.06 | 0.05 | 0.36 | 0.01 | 0.06 | 0.04 | 0.04 | 0.08 | 0.03 | 0.40 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.06 | 0.00 | 0.10 | 0.04 | 0.09 | 0.02 | 0.13 |
| G6PD | ENSG00000160211 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.03 | 0.25 | 0.02 | 0.19 | 0.03 | 0.15 | 0.01 | 0.23 | 0.02 | 0.17 | 0.03 | 0.05 | 0.01 | 0.10 | 0.01 | 0.06 | 0.01 | 0.14 | 0.03 | 0.10 | 0.01 | 0.13 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.10 | 0.03 | 0.47 | 0.13 | 0.23 | 0.02 | 0.12 | 0.04 | 0.09 | 0.10 | 0.24 | 0.13 | 0.01 | 0.03 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.04 | 0.03 | 0.05 | 0.00 | 0.08 | 0.01 |
| SGK1 | ENSG00000118515 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.10 | 0.05 | 0.00 | 0.01 | 0.00 | 0.14 | 0.03 | 0.05 | 0.08 | 0.03 | 0.07 | 0.01 | 0.19 | 0.01 | 0.11 | 0.02 | 0.03 | 0.01 | 0.04 | 0.02 | 0.05 | 0.02 | 0.01 | 0.08 | 0.00 | 0.10 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.06 | 0.08 | 0.29 | 0.03 | 0.03 | 0.04 | 0.02 | 0.12 | 0.03 | 0.33 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.16 | 0.00 | 0.05 | 0.00 | 0.11 | 0.00 | 0.09 | 0.02 | 0.13 |
| ANPEP | ENSG00000166825 | 0.02 | 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 | 0.20 | 0.00 | 0.06 | 0.02 | 0.24 | 0.01 | 0.30 | 0.01 | 0.05 | 0.01 | 0.10 | 0.00 | 0.06 | 0.00 | 0.07 | 0.04 | 0.05 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.02 | 0.33 | 0.07 | 0.18 | 0.00 | 0.05 | 0.02 | 0.26 | 0.05 | 0.12 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.20 | 0.01 |
| GABRG3 | ENSG00000182256 | 0.01 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.03 | 0.04 | 0.06 | 0.11 | 0.00 | 0.00 | 0.00 | 0.26 | 0.02 | 0.11 | 0.06 | 0.11 | 0.06 | 0.04 | 0.08 | 0.10 | 0.01 | 0.09 | 0.01 | 0.09 | 0.01 | 0.07 | 0.01 | 0.05 | 0.01 | 0.03 | 0.00 | 0.07 | 0.07 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.12 | 0.07 | 0.30 | 0.04 | 0.05 | 0.02 | 0.06 | 0.07 | 0.40 | 0.14 | 0.12 | 0.04 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.04 | 0.11 |
| ABCA4 | ENSG00000198691 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.07 | 0.00 | 0.00 | 0.02 | 0.39 | 0.02 | 0.10 | 0.04 | 0.07 | 0.01 | 0.08 | 0.00 | 0.08 | 0.02 | 0.08 | 0.00 | 0.06 | 0.01 | 0.05 | 0.00 | 0.02 | 0.03 | 0.02 | 0.00 | 0.16 | 0.02 | 0.04 | 0.00 | 0.23 | 0.00 | 0.00 | 0.07 | 0.11 | 0.15 | 0.17 | 0.01 | 0.05 | 0.06 | 0.03 | 0.06 | 0.06 | 0.08 | 0.09 | 0.03 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.07 | 0.00 | 0.05 | 0.03 | 0.13 |
| HS3ST1 | ENSG00000002587 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.05 | 0.02 | 0.05 | 0.07 | 0.05 | 0.05 | 0.04 | 0.01 | 0.02 | 0.04 | 0.06 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.20 | 0.08 | 0.01 | 0.03 | 0.04 | 0.02 | 0.11 | 0.00 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 |
| ARSG | ENSG00000141337 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.22 | 0.01 | 0.05 | 0.00 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.07 | 0.02 | 0.22 | 0.03 | 0.12 | 0.04 | 0.08 | 0.01 | 0.09 | 0.02 | 0.05 | 0.10 | 0.23 | 0.02 | 0.12 | 0.01 | 0.15 | 0.18 | 0.02 | 0.01 | 0.00 | 0.00 | 0.56 | 0.01 | 0.26 | 0.04 | 0.16 | 0.03 | 0.13 | 0.01 | 0.45 | 0.02 | 0.22 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.03 | 0.00 | 0.17 | 0.01 | 0.23 | 0.02 |
| PDE1C | ENSG00000154678 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.10 | 0.03 | 0.04 | 0.01 | 0.14 | 0.03 | 0.03 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.15 | 0.11 | 0.04 | 0.00 | 0.06 | 0.01 | 0.04 | 0.00 | 0.15 | 0.04 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.06 | 0.02 |
| MAPK10 | ENSG00000109339 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.12 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.04 | 0.06 | 0.06 | 0.03 | 0.09 | 0.05 | 0.13 | 0.03 | 0.07 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 | 0.13 | 0.00 | 0.03 | 0.06 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.06 | 0.24 | 0.02 | 0.10 | 0.02 | 0.03 | 0.02 | 0.19 | 0.10 | 0.08 | 0.00 | 0.03 | 0.00 | 0.01 | 0.04 | 0.08 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 |
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