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 |
| CHGA | ENSG00000100604 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.05 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.05 | 0.11 | 0.02 | 0.04 | 0.05 | 0.06 | 0.07 | 0.04 | 0.05 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.31 | 0.05 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.19 | 0.17 | 0.07 | 0.09 | 0.06 | 0.03 | 0.10 | 0.04 | 0.10 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| SLC10A1 | ENSG00000100652 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.06 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.04 | 0.02 | 0.05 | 0.03 | 0.01 | 0.05 | 0.03 | 0.02 | 0.04 | 0.03 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.10 | 0.00 | 0.33 | 0.02 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.10 | 0.07 | 0.26 | 0.02 | 0.02 | 0.02 | 0.02 | 0.05 | 0.04 | 0.03 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.08 | 0.03 | 0.00 | 0.01 | 0.04 |
| SERPINA4 | ENSG00000100665 | 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 | 0.12 | 0.02 | 0.05 | 0.04 | 0.07 | 0.06 | 0.03 | 0.05 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.09 | 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 | 0.10 | 0.04 | 0.03 | 0.06 | 0.02 | 0.09 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| BDKRB1 | ENSG00000100739 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.04 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.06 | 0.15 | 0.02 | 0.06 | 0.04 | 0.07 | 0.05 | 0.04 | 0.05 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.31 | 0.15 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.08 | 0.21 | 0.17 | 0.07 | 0.09 | 0.05 | 0.03 | 0.06 | 0.02 | 0.10 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.09 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| PSMC1 | ENSG00000100764 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.05 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.07 | 0.05 | 0.11 | 0.02 | 0.04 | 0.05 | 0.07 | 0.07 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.09 | 0.00 | 0.40 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.18 | 0.16 | 0.07 | 0.07 | 0.04 | 0.01 | 0.08 | 0.05 | 0.05 | 0.11 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| PSMB5 | ENSG00000100804 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.13 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.02 | 0.14 | 0.07 | 0.07 | 0.07 | 0.12 | 0.06 | 0.06 | 0.04 | 0.02 | 0.02 | 0.01 | 0.07 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.29 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.28 | 0.12 | 0.08 | 0.03 | 0.06 | 0.03 | 0.10 | 0.07 | 0.18 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.09 | 0.00 | 0.00 | 0.03 | 0.02 |
| APEX1 | ENSG00000100823 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.04 | 0.18 | 0.07 | 0.08 | 0.06 | 0.12 | 0.07 | 0.08 | 0.04 | 0.03 | 0.02 | 0.01 | 0.10 | 0.01 | 0.04 | 0.09 | 0.00 | 0.00 | 0.02 | 0.18 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.41 | 0.10 | 0.07 | 0.02 | 0.08 | 0.03 | 0.15 | 0.08 | 0.18 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| NFKBIA | ENSG00000100906 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.67 | 0.01 | 0.15 | 0.05 | 0.08 | 0.03 | 0.24 | 0.03 | 0.08 | 0.01 | 0.03 | 0.02 | 0.02 | 0.03 | 0.01 | 0.01 | 0.08 | 0.04 | 0.05 | 0.02 | 0.24 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.16 | 0.02 | 0.19 | 0.11 | 0.07 | 0.01 | 0.06 | 0.02 | 0.26 | 0.03 | 0.21 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.00 | 0.02 | 0.01 |
| GMPR2 | ENSG00000100938 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.16 | 0.03 | 0.10 | 0.07 | 0.05 | 0.07 | 0.11 | 0.06 | 0.05 | 0.05 | 0.02 | 0.02 | 0.01 | 0.06 | 0.00 | 0.03 | 0.08 | 0.01 | 0.00 | 0.02 | 0.28 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.04 | 0.17 | 0.13 | 0.03 | 0.03 | 0.06 | 0.03 | 0.27 | 0.12 | 0.22 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| GSS | ENSG00000100983 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.15 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.15 | 0.01 | 0.15 | 0.00 | 0.07 | 0.01 | 0.05 | 0.00 | 0.12 | 0.00 | 0.16 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.05 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.16 | 0.03 | 0.13 | 0.00 | 0.06 | 0.01 | 0.39 | 0.00 | 0.12 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| PROCR | ENSG00000101000 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.15 | 0.01 | 0.13 | 0.00 | 0.08 | 0.01 | 0.05 | 0.00 | 0.11 | 0.00 | 0.16 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.17 | 0.03 | 0.14 | 0.00 | 0.05 | 0.01 | 0.32 | 0.00 | 0.12 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 |
| R3HDML | ENSG00000101074 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.22 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.07 | 0.01 | 0.02 | 0.02 | 0.13 | 0.00 | 0.21 | 0.00 | 0.22 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.17 | 0.05 | 0.03 | 0.03 | 0.08 | 0.01 | 0.43 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| BMP7 | ENSG00000101144 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.21 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.11 | 0.01 | 0.19 | 0.00 | 0.13 | 0.00 | 0.10 | 0.00 | 0.03 | 0.00 | 0.10 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.39 | 0.01 | 0.39 | 0.04 | 0.04 | 0.02 | 0.10 | 0.01 | 0.21 | 0.00 | 0.21 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.11 | 0.00 |
| CTSZ | ENSG00000101160 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.26 | 0.01 | 0.04 | 0.03 | 0.01 | 0.01 | 0.10 | 0.01 | 0.22 | 0.00 | 0.14 | 0.00 | 0.08 | 0.00 | 0.05 | 0.00 | 0.11 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.38 | 0.02 | 0.37 | 0.05 | 0.03 | 0.03 | 0.10 | 0.01 | 0.17 | 0.00 | 0.26 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.11 | 0.01 |
| TUBB1 | ENSG00000101162 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.26 | 0.01 | 0.04 | 0.03 | 0.01 | 0.01 | 0.10 | 0.01 | 0.22 | 0.00 | 0.14 | 0.00 | 0.08 | 0.00 | 0.05 | 0.00 | 0.11 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.38 | 0.02 | 0.38 | 0.05 | 0.03 | 0.03 | 0.10 | 0.01 | 0.17 | 0.00 | 0.26 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.11 | 0.01 |
| HRH3 | ENSG00000101180 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.06 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.28 | 0.01 | 0.07 | 0.04 | 0.02 | 0.01 | 0.12 | 0.01 | 0.18 | 0.00 | 0.08 | 0.01 | 0.12 | 0.01 | 0.03 | 0.00 | 0.13 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.35 | 0.02 | 0.48 | 0.04 | 0.04 | 0.03 | 0.15 | 0.01 | 0.43 | 0.00 | 0.26 | 0.07 | 0.03 | 0.01 | 0.03 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.11 | 0.00 |
| AVP | ENSG00000101200 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.13 | 0.01 | 0.03 | 0.03 | 0.07 | 0.03 | 0.04 | 0.01 | 0.06 | 0.04 | 0.06 | 0.09 | 0.00 | 0.03 | 0.04 | 0.01 | 0.00 | 0.03 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.33 | 0.07 | 0.04 | 0.02 | 0.09 | 0.03 | 0.09 | 0.07 | 0.07 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 |
| COL20A1 | ENSG00000101203 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.29 | 0.01 | 0.06 | 0.04 | 0.03 | 0.01 | 0.16 | 0.01 | 0.16 | 0.00 | 0.08 | 0.00 | 0.11 | 0.01 | 0.03 | 0.00 | 0.12 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.33 | 0.02 | 0.49 | 0.04 | 0.04 | 0.03 | 0.13 | 0.01 | 0.34 | 0.00 | 0.18 | 0.08 | 0.03 | 0.03 | 0.03 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.00 |
| CHRNA4 | ENSG00000101204 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.29 | 0.01 | 0.06 | 0.04 | 0.03 | 0.01 | 0.16 | 0.01 | 0.16 | 0.00 | 0.08 | 0.00 | 0.11 | 0.01 | 0.02 | 0.00 | 0.12 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.33 | 0.02 | 0.49 | 0.04 | 0.04 | 0.03 | 0.13 | 0.01 | 0.34 | 0.00 | 0.18 | 0.08 | 0.03 | 0.03 | 0.03 | 0.00 | 0.04 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.00 |
| PTK6 | ENSG00000101213 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.32 | 0.01 | 0.08 | 0.04 | 0.03 | 0.01 | 0.17 | 0.01 | 0.16 | 0.00 | 0.08 | 0.00 | 0.13 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.34 | 0.02 | 0.51 | 0.04 | 0.04 | 0.02 | 0.15 | 0.01 | 0.44 | 0.00 | 0.20 | 0.11 | 0.03 | 0.03 | 0.03 | 0.00 | 0.04 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.15 | 0.00 |
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