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 |
| ODC1 | ENSG00000115758 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.06 | 0.03 | 0.01 | 0.14 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.05 | 0.02 | 0.09 | 0.05 | 0.02 | 0.04 | 0.08 | 0.06 | 0.04 | 0.03 | 0.01 | 0.01 | 0.02 | 0.05 | 0.01 | 0.03 | 0.13 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.05 | 0.25 | 0.16 | 0.08 | 0.01 | 0.11 | 0.03 | 0.36 | 0.07 | 0.05 | 0.10 | 0.16 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.02 | 0.01 | 0.05 | 0.02 | 0.05 | 0.00 | 0.02 | 0.04 |
| SLC25A12 | ENSG00000115840 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.13 | 0.02 | 0.13 | 0.01 | 0.25 | 0.01 | 0.04 | 0.03 | 0.01 | 0.01 | 0.03 | 0.02 | 0.03 | 0.02 | 0.06 | 0.06 | 0.05 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.37 | 0.04 | 0.09 | 0.01 | 0.06 | 0.01 | 0.16 | 0.00 | 0.06 | 0.10 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 |
| PLCL1 | ENSG00000115896 | 0.03 | 0.02 | 0.07 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.09 | 0.00 | 0.00 | 0.02 | 0.05 | 0.03 | 0.02 | 0.16 | 0.05 | 0.13 | 0.07 | 0.15 | 0.04 | 0.06 | 0.03 | 0.03 | 0.01 | 0.03 | 0.00 | 0.07 | 0.00 | 0.06 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.03 | 0.31 | 0.06 | 0.14 | 0.06 | 0.05 | 0.01 | 0.06 | 0.04 | 0.07 | 0.07 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 |
| SLC1A4 | ENSG00000115902 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.30 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.05 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.20 | 0.04 | 0.03 | 0.00 | 0.05 | 0.01 | 0.21 | 0.00 | 0.06 | 0.04 | 0.03 | 0.04 | 0.00 | 0.00 | 0.29 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| KYNU | ENSG00000115919 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.17 | 0.05 | 0.06 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.02 | 0.08 | 0.03 | 0.04 | 0.02 | 0.08 | 0.06 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.02 | 0.07 | 0.05 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.06 | 0.13 | 0.11 | 0.03 | 0.03 | 0.03 | 0.01 | 0.02 | 0.00 | 0.11 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| PLEK | ENSG00000115956 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.20 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.06 | 0.02 | 0.06 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.16 | 0.04 | 0.03 | 0.00 | 0.05 | 0.01 | 0.13 | 0.00 | 0.05 | 0.04 | 0.03 | 0.04 | 0.01 | 0.00 | 0.04 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| PCYOX1 | ENSG00000116005 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.01 | 0.15 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.08 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.13 | 0.04 | 0.03 | 0.00 | 0.05 | 0.01 | 0.20 | 0.00 | 0.06 | 0.04 | 0.04 | 0.05 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
| KISS1R | ENSG00000116014 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.14 | 0.05 | 0.00 | 0.03 | 0.10 | 0.04 | 0.09 | 0.03 | 0.16 | 0.01 | 0.15 | 0.06 | 0.18 | 0.05 | 0.08 | 0.01 | 0.06 | 0.02 | 0.09 | 0.01 | 0.07 | 0.02 | 0.14 | 0.04 | 0.03 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.92 | 0.04 | 0.24 | 0.03 | 0.25 | 0.00 | 0.81 | 0.25 | 0.21 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.08 | 0.01 | 0.08 | 0.01 | 0.01 | 0.04 | 0.03 | 0.08 |
| CD207 | ENSG00000116031 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.07 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.08 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.12 | 0.04 | 0.03 | 0.00 | 0.04 | 0.01 | 0.17 | 0.00 | 0.06 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
| ATP6V1B1 | ENSG00000116039 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.07 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.08 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.12 | 0.04 | 0.03 | 0.00 | 0.04 | 0.01 | 0.17 | 0.00 | 0.06 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
| MSH6 | ENSG00000116062 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.01 | 0.26 | 0.02 | 0.04 | 0.01 | 0.04 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.04 | 0.01 | 0.00 | 0.08 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.28 | 0.05 | 0.04 | 0.00 | 0.06 | 0.02 | 0.04 | 0.02 | 0.06 | 0.06 | 0.13 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 |
| SPR | ENSG00000116096 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.01 | 0.13 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.01 | 0.15 | 0.04 | 0.03 | 0.00 | 0.04 | 0.01 | 0.10 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| GPX7 | ENSG00000116157 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.06 | 0.08 | 0.04 | 0.00 | 0.00 | 0.06 | 0.04 | 0.07 | 0.04 | 0.05 | 0.03 | 0.04 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.01 | 0.04 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.06 | 0.00 | 0.25 | 0.02 | 0.03 | 0.00 | 0.17 | 0.00 | 0.00 | 0.06 | 0.04 | 0.28 | 0.10 | 0.08 | 0.02 | 0.05 | 0.02 | 0.04 | 0.04 | 0.21 | 0.04 | 0.07 | 0.04 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.06 | 0.03 |
| TPSG1 | ENSG00000116176 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.05 | 0.04 | 0.09 | 0.03 | 0.03 | 0.03 | 0.12 | 0.04 | 0.08 | 0.03 | 0.04 | 0.03 | 0.03 | 0.01 | 0.02 | 0.04 | 0.06 | 0.00 | 0.05 | 0.18 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.11 | 0.19 | 0.10 | 0.05 | 0.04 | 0.04 | 0.17 | 0.21 | 0.08 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 |
| ICMT | ENSG00000116237 | 0.00 | 0.06 | 0.01 | 0.10 | 0.00 | 0.00 | 0.01 | 0.05 | 0.10 | 0.09 | 0.00 | 0.02 | 0.04 | 0.31 | 0.07 | 0.05 | 0.08 | 0.11 | 0.06 | 0.09 | 0.18 | 0.09 | 0.10 | 0.10 | 0.02 | 0.14 | 0.00 | 0.20 | 0.04 | 0.06 | 0.02 | 0.32 | 0.00 | 1.09 | 0.03 | 0.21 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.26 | 0.35 | 0.06 | 0.10 | 0.07 | 0.12 | 0.13 | 0.27 | 0.17 | 0.25 | 0.09 | 0.12 | 0.02 | 0.01 | 0.04 | 0.15 | 0.00 | 0.07 | 0.02 | 0.29 | 0.00 | 0.05 | 0.06 | 0.16 |
| CHD5 | ENSG00000116254 | 0.00 | 0.06 | 0.01 | 0.10 | 0.00 | 0.00 | 0.01 | 0.05 | 0.10 | 0.09 | 0.00 | 0.02 | 0.04 | 0.31 | 0.07 | 0.06 | 0.08 | 0.11 | 0.06 | 0.09 | 0.17 | 0.09 | 0.10 | 0.09 | 0.02 | 0.15 | 0.00 | 0.20 | 0.04 | 0.06 | 0.02 | 0.32 | 0.00 | 1.09 | 0.03 | 0.21 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.26 | 0.35 | 0.06 | 0.10 | 0.06 | 0.12 | 0.11 | 0.27 | 0.17 | 0.25 | 0.08 | 0.12 | 0.02 | 0.01 | 0.00 | 0.18 | 0.00 | 0.07 | 0.02 | 0.29 | 0.00 | 0.05 | 0.06 | 0.16 |
| QSOX1 | ENSG00000116260 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.22 | 0.02 | 0.02 | 0.00 | 0.09 | 0.03 | 0.11 | 0.00 | 0.17 | 0.01 | 0.03 | 0.00 | 0.19 | 0.02 | 0.10 | 0.01 | 0.03 | 0.00 | 0.11 | 0.03 | 0.04 | 0.00 | 0.16 | 0.01 | 0.17 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 | 0.36 | 0.03 | 0.08 | 0.01 | 0.10 | 0.00 | 0.29 | 0.00 | 0.22 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.32 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.11 | 0.03 |
| PHF13 | ENSG00000116273 | 0.00 | 0.06 | 0.01 | 0.09 | 0.00 | 0.00 | 0.01 | 0.05 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.31 | 0.07 | 0.05 | 0.08 | 0.11 | 0.06 | 0.08 | 0.18 | 0.07 | 0.09 | 0.09 | 0.02 | 0.15 | 0.00 | 0.20 | 0.04 | 0.06 | 0.03 | 0.30 | 0.00 | 1.09 | 0.03 | 0.23 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.26 | 0.34 | 0.06 | 0.10 | 0.07 | 0.11 | 0.08 | 0.27 | 0.17 | 0.25 | 0.08 | 0.12 | 0.02 | 0.01 | 0.00 | 0.15 | 0.00 | 0.06 | 0.03 | 0.28 | 0.00 | 0.05 | 0.07 | 0.13 |
| PARK7 | ENSG00000116288 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.04 | 0.10 | 0.08 | 0.00 | 0.03 | 0.04 | 0.29 | 0.06 | 0.05 | 0.06 | 0.11 | 0.05 | 0.08 | 0.10 | 0.09 | 0.08 | 0.10 | 0.01 | 0.15 | 0.00 | 0.20 | 0.05 | 0.07 | 0.03 | 0.32 | 0.00 | 1.10 | 0.03 | 0.26 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.23 | 0.37 | 0.04 | 0.11 | 0.06 | 0.11 | 0.06 | 0.27 | 0.17 | 0.23 | 0.08 | 0.12 | 0.02 | 0.01 | 0.00 | 0.11 | 0.00 | 0.07 | 0.02 | 0.32 | 0.00 | 0.07 | 0.07 | 0.12 |
| OPRD1 | ENSG00000116329 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.03 | 0.06 | 0.08 | 0.00 | 0.01 | 0.05 | 0.17 | 0.04 | 0.06 | 0.03 | 0.08 | 0.03 | 0.06 | 0.06 | 0.11 | 0.03 | 0.11 | 0.00 | 0.16 | 0.00 | 0.21 | 0.00 | 0.09 | 0.01 | 0.21 | 0.00 | 0.96 | 0.02 | 0.07 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.15 | 0.12 | 0.38 | 0.04 | 0.05 | 0.03 | 0.12 | 0.16 | 0.08 | 0.12 | 0.08 | 0.04 | 0.04 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.03 | 0.05 | 0.00 | 0.07 | 0.08 | 0.05 |
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