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 |
| GABRA1 | ENSG00000022355 | 0.31 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.08 | 0.04 | 0.04 | 0.02 | 0.04 | 0.01 | 0.05 | 0.04 | 0.01 | 0.03 | 0.04 | 0.01 | 0.02 | 0.04 | 0.05 | 0.02 | 0.01 | 0.10 | 0.03 | 0.09 | 0.01 | 0.32 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.04 | 0.17 | 0.16 | 0.03 | 0.02 | 0.03 | 0.03 | 0.15 | 0.01 | 0.12 | 0.09 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.08 | 0.01 | 0.05 | 0.04 | 0.00 | 0.01 | 0.12 |
| DUSP12 | ENSG00000081721 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.79 | 0.01 | 0.02 | 0.00 | 0.10 | 0.01 | 0.28 | 0.00 | 0.27 | 0.00 | 0.05 | 0.00 | 0.28 | 0.01 | 0.12 | 0.01 | 0.03 | 0.00 | 0.14 | 0.00 | 0.06 | 0.00 | 0.30 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.31 | 0.01 | 0.37 | 0.02 | 0.16 | 0.01 | 0.13 | 0.00 | 0.28 | 0.00 | 0.37 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 |
| OPCML | ENSG00000183715 | 0.00 | 0.01 | 0.00 | 0.04 | 0.05 | 0.05 | 0.02 | 0.04 | 0.03 | 0.12 | 0.00 | 0.00 | 0.11 | 0.06 | 0.05 | 0.11 | 0.07 | 0.14 | 0.05 | 0.15 | 0.11 | 0.20 | 0.05 | 0.09 | 0.02 | 0.02 | 0.03 | 0.02 | 0.03 | 0.02 | 0.04 | 0.10 | 0.00 | 0.31 | 0.02 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.22 | 0.28 | 0.21 | 0.04 | 0.31 | 0.04 | 0.08 | 0.08 | 0.19 | 0.08 | 0.26 | 0.00 | 0.30 | 0.04 | 0.00 | 0.13 | 0.00 | 0.06 | 0.03 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.26 |
| GIPR | ENSG00000010310 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.14 | 0.03 | 0.00 | 0.02 | 0.03 | 0.05 | 0.10 | 0.07 | 0.10 | 0.09 | 0.02 | 0.02 | 0.06 | 0.04 | 0.09 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.09 | 0.02 | 0.05 | 0.04 | 0.12 | 0.03 | 0.18 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.05 | 0.11 | 0.30 | 0.07 | 0.05 | 0.11 | 0.04 | 0.29 | 0.19 | 0.06 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.00 | 0.13 | 0.02 | 0.12 | 0.00 | 0.00 | 0.02 | 0.03 |
| CRELD2 | ENSG00000184164 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.03 | 0.00 | 0.06 | 0.02 | 0.12 | 0.06 | 0.09 | 0.02 | 0.04 | 0.03 | 0.03 | 0.03 | 0.07 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.10 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.06 | 0.06 | 0.02 | 0.64 | 0.03 | 0.07 | 0.03 | 0.15 | 0.06 | 0.27 | 0.06 | 0.15 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.00 | 0.12 | 0.05 |
| PLXNC1 | ENSG00000136040 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.05 | 0.00 | 0.07 | 0.04 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.05 | 0.04 | 0.03 | 0.01 | 0.03 | 0.03 | 0.06 | 0.02 | 0.03 | 0.00 | 0.03 | 0.01 | 0.05 | 0.02 | 0.06 | 0.03 | 0.03 | 0.00 | 0.17 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.06 | 0.06 | 0.23 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.14 | 0.31 | 0.07 | 0.00 | 0.01 | 0.00 | 0.02 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.05 | 0.00 | 0.01 | 0.08 |
| PIK3R4 | ENSG00000196455 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.02 | 0.15 | 0.01 | 0.08 | 0.00 | 0.16 | 0.02 | 0.06 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 | 0.30 | 0.04 | 0.13 | 0.00 | 0.07 | 0.00 | 0.18 | 0.03 | 0.03 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.05 |
| IL11RA | ENSG00000137070 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.05 | 0.02 | 0.36 | 0.04 | 0.21 | 0.03 | 0.25 | 0.01 | 0.16 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.04 | 0.01 | 0.24 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.10 | 0.06 | 0.01 | 0.01 | 0.03 | 0.02 | 0.01 | 0.05 | 0.11 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.07 | 0.00 | 0.03 | 0.07 | 0.05 |
| SLC25A32 | ENSG00000164933 | 0.01 | 0.00 | 0.01 | 0.00 | 0.21 | 0.00 | 0.07 | 0.01 | 0.46 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.19 | 0.01 | 0.24 | 0.02 | 0.17 | 0.00 | 0.35 | 0.00 | 0.24 | 0.00 | 0.12 | 0.01 | 0.19 | 0.00 | 0.05 | 0.01 | 0.31 | 0.00 | 0.25 | 0.01 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.48 | 0.00 | 0.74 | 0.07 | 0.15 | 0.00 | 0.11 | 0.01 | 0.44 | 0.00 | 0.14 | 0.06 | 0.08 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.13 | 0.00 | 0.01 | 0.00 | 0.42 | 0.00 | 0.14 | 0.01 |
| ADAMTS19 | ENSG00000145808 | 0.27 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.07 | 0.00 | 0.07 | 0.00 | 0.05 | 0.02 | 0.10 | 0.01 | 0.11 | 0.01 | 0.06 | 0.02 | 0.05 | 0.00 | 0.04 | 0.07 | 0.04 | 0.09 | 0.01 | 0.27 | 0.03 | 0.02 | 0.03 | 0.01 | 0.00 | 0.03 | 0.05 | 0.09 | 0.21 | 0.02 | 0.03 | 0.01 | 0.02 | 0.10 | 0.06 | 0.05 | 0.06 | 0.01 | 0.01 | 0.00 | 0.09 | 0.04 | 0.02 | 0.00 | 0.04 | 0.01 | 0.03 | 0.00 | 0.03 | 0.02 | 0.08 |
| PTPN11 | ENSG00000179295 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.03 | 0.04 | 0.16 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.05 | 0.04 | 0.04 | 0.01 | 0.03 | 0.09 | 0.05 | 0.06 | 0.02 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.06 | 0.02 | 0.05 | 0.00 | 0.26 | 0.10 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.11 | 0.22 | 0.02 | 0.02 | 0.03 | 0.05 | 0.08 | 0.08 | 0.21 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.06 |
| REG3A | ENSG00000172016 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.12 | 0.02 | 0.05 | 0.02 | 0.08 | 0.04 | 0.03 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.13 | 0.05 | 0.04 | 0.01 | 0.05 | 0.01 | 0.17 | 0.06 | 0.12 | 0.04 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| PRKCD | ENSG00000163932 | 0.00 | 0.15 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.15 | 0.00 | 0.03 | 0.00 | 0.55 | 0.02 | 0.06 | 0.01 | 0.11 | 0.00 | 0.06 | 0.05 | 0.13 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.04 | 0.04 | 0.06 | 0.00 | 0.20 | 0.18 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.16 | 0.10 | 0.21 | 0.00 | 0.07 | 0.06 | 0.07 | 0.04 | 0.32 | 0.03 | 0.15 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.05 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.04 |
| PTGS1 | ENSG00000095303 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.05 | 0.02 | 0.06 | 0.01 | 0.10 | 0.01 | 0.08 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.11 | 0.15 | 0.02 | 0.01 | 0.02 | 0.03 | 0.03 | 0.16 | 0.12 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 |
| ATP13A3 | ENSG00000133657 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.05 | 0.17 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.14 | 0.06 | 1.35 | 0.01 | 0.57 | 0.00 | 0.76 | 0.02 | 0.24 | 0.02 | 0.05 | 0.01 | 0.06 | 0.01 | 0.03 | 0.01 | 0.12 | 0.03 | 0.18 | 0.03 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.21 | 0.02 | 0.99 | 0.08 | 0.65 | 0.00 | 0.37 | 0.00 | 0.80 | 0.15 | 0.13 | 0.11 | 0.16 | 0.02 | 0.00 | 0.00 | 0.16 | 0.04 | 0.02 | 0.05 | 0.07 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| TNFRSF1B | ENSG00000028137 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.05 | 0.09 | 0.07 | 0.00 | 0.02 | 0.04 | 0.26 | 0.06 | 0.05 | 0.05 | 0.11 | 0.04 | 0.08 | 0.14 | 0.08 | 0.11 | 0.08 | 0.01 | 0.13 | 0.00 | 0.20 | 0.03 | 0.06 | 0.03 | 0.22 | 0.00 | 1.07 | 0.04 | 0.12 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.19 | 0.22 | 0.36 | 0.06 | 0.10 | 0.07 | 0.10 | 0.03 | 0.25 | 0.19 | 0.19 | 0.08 | 0.09 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.07 | 0.12 | 0.00 | 0.07 | 0.06 | 0.11 |
| SULT1B1 | ENSG00000173597 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.12 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.03 | 0.23 | 0.01 | 0.08 | 0.02 | 0.14 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.03 | 0.07 | 0.00 | 0.03 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.26 | 0.08 | 0.04 | 0.04 | 0.04 | 0.01 | 0.06 | 0.05 | 0.07 | 0.05 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| SLC16A10 | ENSG00000112394 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.29 | 0.02 | 0.13 | 0.00 | 0.01 | 0.00 | 0.14 | 0.01 | 0.05 | 0.04 | 0.04 | 0.02 | 0.03 | 0.05 | 0.09 | 0.05 | 0.08 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.15 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.09 | 0.07 | 0.25 | 0.04 | 0.02 | 0.08 | 0.02 | 0.10 | 0.04 | 0.20 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.21 | 0.00 | 0.02 | 0.02 | 0.06 | 0.06 | 0.03 | 0.00 | 0.14 |
| SLC46A2 | ENSG00000119457 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.04 | 0.01 | 0.05 | 0.00 | 0.11 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.04 | 0.06 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.09 | 0.11 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.15 | 0.06 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 |
| RECQL | ENSG00000004700 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.06 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.18 | 0.04 | 0.17 | 0.01 | 0.08 | 0.01 | 0.15 | 0.01 | 0.13 | 0.03 | 0.02 | 0.01 | 0.07 | 0.03 | 0.08 | 0.04 | 0.00 | 0.04 | 0.14 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.32 | 0.06 | 0.01 | 0.01 | 0.05 | 0.01 | 0.17 | 0.03 | 0.14 | 0.09 | 0.63 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.07 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.05 | 0.01 |
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