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 |
| MGEA5 | ENSG00000198408 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.01 | 0.10 | 0.00 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.01 | 0.07 | 0.00 | 0.05 | 0.03 | 0.08 | 0.03 | 0.08 | 0.01 | 0.10 | 0.00 | 0.07 | 0.03 | 0.03 | 0.01 | 0.07 | 0.11 | 0.14 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.08 | 0.06 | 0.32 | 0.01 | 0.07 | 0.03 | 0.09 | 0.05 | 0.09 | 0.05 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.04 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.04 |
| CHID1 | ENSG00000177830 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.05 | 0.04 | 0.07 | 0.01 | 0.17 | 0.03 | 0.06 | 0.06 | 0.13 | 0.03 | 0.07 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.06 | 0.06 | 0.04 | 0.03 | 0.01 | 0.08 | 0.06 | 0.02 | 0.06 | 0.00 | 0.00 | 0.04 | 0.13 | 0.05 | 0.49 | 0.01 | 0.07 | 0.06 | 0.09 | 0.10 | 0.15 | 0.02 | 0.22 | 0.03 | 0.05 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.11 | 0.01 | 0.06 | 0.00 | 0.00 | 0.02 | 0.04 |
| A1BG | ENSG00000121410 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.07 | 0.13 | 0.09 | 0.07 | 0.05 | 0.25 | 0.06 | 0.15 | 0.03 | 0.02 | 0.03 | 0.02 | 0.04 | 0.05 | 0.04 | 0.07 | 0.03 | 0.02 | 0.07 | 0.14 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.15 | 0.06 | 0.18 | 0.35 | 0.12 | 0.05 | 0.08 | 0.07 | 0.14 | 0.12 | 0.07 | 0.30 | 0.00 | 0.06 | 0.02 | 0.01 | 0.16 | 0.03 | 0.01 | 0.17 | 0.05 | 0.12 | 0.00 | 0.00 | 0.04 | 0.06 |
| ATRN | ENSG00000088812 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.04 | 0.13 | 0.01 | 0.03 | 0.03 | 0.07 | 0.03 | 0.05 | 0.01 | 0.06 | 0.04 | 0.05 | 0.08 | 0.00 | 0.03 | 0.05 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 | 0.29 | 0.07 | 0.04 | 0.01 | 0.10 | 0.03 | 0.11 | 0.07 | 0.09 | 0.08 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 |
| PKN1 | ENSG00000123143 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.06 | 0.02 | 0.00 | 0.04 | 0.13 | 0.04 | 0.05 | 0.01 | 0.14 | 0.04 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.07 | 0.05 | 0.05 | 0.03 | 0.26 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.87 | 0.06 | 0.08 | 0.02 | 0.22 | 0.02 | 0.25 | 0.11 | 0.17 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 |
| NRD1 | ENSG00000078618 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.10 | 0.04 | 0.00 | 0.00 | 0.06 | 0.04 | 0.08 | 0.04 | 0.06 | 0.03 | 0.05 | 0.03 | 0.03 | 0.04 | 0.02 | 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 | 0.16 | 0.00 | 0.00 | 0.06 | 0.05 | 0.29 | 0.10 | 0.08 | 0.01 | 0.04 | 0.02 | 0.03 | 0.03 | 0.21 | 0.02 | 0.08 | 0.04 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.04 | 0.00 | 0.07 | 0.04 | 0.03 |
| ENTPD1 | ENSG00000138185 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.12 | 0.02 | 0.10 | 0.00 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.05 | 0.02 | 0.10 | 0.01 | 0.10 | 0.00 | 0.09 | 0.00 | 0.07 | 0.01 | 0.03 | 0.02 | 0.06 | 0.16 | 0.14 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.07 | 0.09 | 0.31 | 0.01 | 0.07 | 0.02 | 0.10 | 0.03 | 0.09 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 |
| CAPNS1 | ENSG00000126247 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.01 | 0.18 | 0.03 | 0.00 | 0.00 | 0.06 | 0.03 | 0.23 | 0.01 | 0.44 | 0.03 | 0.04 | 0.02 | 0.21 | 0.02 | 0.09 | 0.03 | 0.05 | 0.00 | 0.04 | 0.00 | 0.09 | 0.00 | 0.03 | 0.01 | 0.12 | 0.03 | 0.04 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.13 | 0.02 | 0.64 | 0.07 | 0.20 | 0.02 | 0.15 | 0.02 | 1.11 | 0.05 | 0.23 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.08 | 0.00 | 0.02 | 0.02 | 0.04 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 |
| ADCY6 | ENSG00000174233 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.04 | 0.02 | 0.01 | 0.04 | 0.06 | 0.04 | 0.06 | 0.04 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.04 | 0.03 | 0.01 | 0.09 | 0.01 | 0.16 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.08 | 0.06 | 0.02 | 0.00 | 0.03 | 0.01 | 0.13 | 0.13 | 0.08 | 0.09 | 0.02 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.01 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.06 | 0.05 |
| ATP4A | ENSG00000105675 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.19 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.27 | 0.00 | 0.43 | 0.03 | 0.08 | 0.01 | 0.22 | 0.03 | 0.08 | 0.04 | 0.05 | 0.00 | 0.04 | 0.00 | 0.10 | 0.00 | 0.05 | 0.02 | 0.13 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.02 | 0.64 | 0.05 | 0.21 | 0.02 | 0.19 | 0.02 | 1.50 | 0.01 | 0.30 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.04 | 0.01 |
| TRAP1 | ENSG00000126602 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.21 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.04 | 0.03 | 0.10 | 0.03 | 0.03 | 0.01 | 0.07 | 0.03 | 0.09 | 0.03 | 0.03 | 0.02 | 0.03 | 0.02 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.12 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.03 | 0.08 | 0.25 | 0.12 | 0.02 | 0.02 | 0.07 | 0.00 | 0.10 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 |
| SLC30A5 | ENSG00000145740 | 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 | 0.10 | 0.01 | 0.07 | 0.01 | 0.16 | 0.01 | 0.14 | 0.01 | 0.07 | 0.00 | 0.09 | 0.00 | 0.07 | 0.00 | 0.04 | 0.00 | 0.13 | 0.08 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.01 | 0.72 | 0.00 | 0.07 | 0.00 | 0.11 | 0.00 | 0.35 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 |
| KDM4A | ENSG00000066135 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.14 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.08 | 0.02 | 0.12 | 0.02 | 0.08 | 0.01 | 0.16 | 0.04 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.04 | 0.08 | 0.00 | 0.27 | 0.02 | 0.03 | 0.02 | 0.10 | 0.00 | 0.00 | 0.09 | 0.04 | 0.54 | 0.06 | 0.10 | 0.01 | 0.12 | 0.01 | 0.20 | 0.05 | 0.11 | 0.03 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.04 | 0.02 |
| PARP14 | ENSG00000173193 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.02 | 0.11 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.25 | 0.04 | 0.06 | 0.01 | 0.04 | 0.01 | 0.05 | 0.09 | 0.10 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 |
| PSAP | ENSG00000197746 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.04 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.04 | 0.04 | 0.02 | 0.07 | 0.02 | 0.15 | 0.02 | 0.03 | 0.03 | 0.09 | 0.05 | 0.01 | 0.02 | 0.03 | 0.02 | 0.25 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.18 | 0.12 | 0.01 | 0.01 | 0.08 | 0.03 | 0.16 | 0.03 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 |
| CELA2A | ENSG00000142615 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.09 | 0.08 | 0.00 | 0.03 | 0.04 | 0.26 | 0.06 | 0.06 | 0.06 | 0.11 | 0.04 | 0.09 | 0.12 | 0.09 | 0.08 | 0.08 | 0.01 | 0.14 | 0.00 | 0.21 | 0.02 | 0.06 | 0.02 | 0.21 | 0.00 | 1.11 | 0.01 | 0.11 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.20 | 0.17 | 0.38 | 0.06 | 0.08 | 0.08 | 0.11 | 0.04 | 0.25 | 0.19 | 0.17 | 0.05 | 0.09 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.02 | 0.05 | 0.09 | 0.00 | 0.07 | 0.06 | 0.09 |
| RHAG | ENSG00000112077 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.01 | 0.20 | 0.04 | 0.05 | 0.03 | 0.32 | 0.02 | 0.14 | 0.02 | 0.04 | 0.01 | 0.12 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.22 | 0.06 | 0.08 | 0.04 | 0.04 | 0.01 | 0.20 | 0.03 | 0.08 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.02 |
| SLC30A6 | ENSG00000152683 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.05 | 0.02 | 0.10 | 0.01 | 0.03 | 0.01 | 0.05 | 0.05 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.06 | 0.00 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.22 | 0.06 | 0.08 | 0.00 | 0.09 | 0.02 | 0.33 | 0.00 | 0.07 | 0.05 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 |
| HAT1 | ENSG00000128708 | 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 | 0.23 | 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 | 0.03 | 0.09 | 0.01 | 0.06 | 0.01 | 0.16 | 0.00 | 0.03 | 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 |
| RIOK3 | ENSG00000101782 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.13 | 0.01 | 0.22 | 0.02 | 0.17 | 0.03 | 0.46 | 0.02 | 0.26 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.24 | 0.01 | 0.00 | 0.01 | 0.04 | 0.03 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.31 | 0.04 | 0.02 | 0.03 | 0.10 | 0.00 | 0.00 | 0.07 | 0.09 | 0.03 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 |
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