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 |
| GPR157 | ENSG00000180758 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.06 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.06 | 0.06 | 0.07 | 0.11 | 0.05 | 0.08 | 0.11 | 0.09 | 0.10 | 0.08 | 0.02 | 0.14 | 0.00 | 0.20 | 0.04 | 0.07 | 0.03 | 0.29 | 0.00 | 1.10 | 0.05 | 0.23 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.23 | 0.35 | 0.04 | 0.10 | 0.06 | 0.11 | 0.04 | 0.27 | 0.18 | 0.22 | 0.08 | 0.11 | 0.02 | 0.01 | 0.00 | 0.07 | 0.00 | 0.06 | 0.01 | 0.27 | 0.00 | 0.10 | 0.06 | 0.12 |
| EIF2AK1 | ENSG00000086232 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.17 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.11 | 0.01 | 0.13 | 0.01 | 0.10 | 0.01 | 0.20 | 0.02 | 0.13 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.01 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.09 | 0.41 | 0.02 | 0.02 | 0.03 | 0.06 | 0.09 | 0.03 | 0.23 | 0.04 | 0.18 | 0.01 | 0.00 | 0.01 | 0.10 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.17 | 0.01 |
| DPF1 | ENSG00000011332 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.34 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.21 | 0.02 | 0.56 | 0.03 | 0.07 | 0.02 | 0.17 | 0.03 | 0.10 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.16 | 0.00 | 0.03 | 0.02 | 0.12 | 0.03 | 0.05 | 0.04 | 0.02 | 0.02 | 0.00 | 0.00 | 0.17 | 0.02 | 0.67 | 0.12 | 0.29 | 0.03 | 0.18 | 0.03 | 1.07 | 0.09 | 0.20 | 0.09 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.03 | 0.00 | 0.00 | 0.05 | 0.02 |
| SPN | ENSG00000197471 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.08 | 0.01 | 0.03 | 0.01 | 0.08 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.07 | 0.03 | 0.02 | 0.02 | 0.08 | 0.01 | 0.34 | 0.05 | 0.04 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| EFEMP1 | ENSG00000115380 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.10 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.01 | 0.28 | 0.01 | 0.04 | 0.01 | 0.07 | 0.03 | 0.02 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.22 | 0.04 | 0.03 | 0.01 | 0.04 | 0.01 | 0.16 | 0.02 | 0.07 | 0.05 | 0.07 | 0.02 | 0.00 | 0.00 | 0.17 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 |
| ITK | ENSG00000113263 | 0.31 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.07 | 0.04 | 0.04 | 0.01 | 0.04 | 0.01 | 0.04 | 0.04 | 0.02 | 0.02 | 0.04 | 0.01 | 0.02 | 0.03 | 0.03 | 0.02 | 0.02 | 0.09 | 0.02 | 0.09 | 0.01 | 0.21 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.04 | 0.16 | 0.14 | 0.03 | 0.02 | 0.02 | 0.02 | 0.05 | 0.02 | 0.06 | 0.06 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.03 | 0.00 | 0.03 | 0.02 | 0.12 |
| CD44 | ENSG00000026508 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.15 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 | 0.07 | 0.02 | 0.15 | 0.02 | 0.17 | 0.01 | 0.32 | 0.04 | 0.28 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.02 | 0.05 | 0.01 | 0.00 | 0.16 | 0.01 | 0.20 | 0.06 | 0.15 | 0.00 | 0.06 | 0.02 | 0.19 | 0.02 | 0.14 | 0.09 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.01 |
| DERL1 | ENSG00000136986 | 0.02 | 0.00 | 0.01 | 0.00 | 0.09 | 0.00 | 0.07 | 0.01 | 0.27 | 0.02 | 0.02 | 0.00 | 0.05 | 0.01 | 0.25 | 0.01 | 0.33 | 0.01 | 0.26 | 0.00 | 0.54 | 0.01 | 0.26 | 0.00 | 0.18 | 0.00 | 0.25 | 0.00 | 0.14 | 0.00 | 0.41 | 0.01 | 0.25 | 0.01 | 0.14 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.52 | 0.02 | 1.38 | 0.04 | 0.17 | 0.01 | 0.19 | 0.01 | 0.25 | 0.00 | 0.16 | 0.05 | 0.03 | 0.02 | 0.02 | 0.00 | 0.13 | 0.00 | 0.20 | 0.00 | 0.04 | 0.01 | 0.53 | 0.00 | 0.19 | 0.01 |
| ACPP | ENSG00000014257 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.01 | 0.17 | 0.01 | 0.13 | 0.00 | 0.16 | 0.03 | 0.07 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.03 | 0.33 | 0.04 | 0.12 | 0.01 | 0.08 | 0.00 | 0.22 | 0.03 | 0.03 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.05 |
| KLHL22 | ENSG00000099910 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.19 | 0.06 | 0.03 | 0.01 | 0.04 | 0.05 | 0.14 | 0.03 | 0.29 | 0.07 | 0.08 | 0.03 | 0.06 | 0.07 | 0.08 | 0.04 | 0.02 | 0.01 | 0.05 | 0.03 | 0.00 | 0.02 | 0.03 | 0.03 | 0.03 | 0.10 | 0.06 | 0.14 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.25 | 0.07 | 0.04 | 0.01 | 0.08 | 0.06 | 0.43 | 0.04 | 0.21 | 0.07 | 0.29 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.14 | 0.03 |
| CA4 | ENSG00000167434 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.28 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.14 | 0.01 | 0.15 | 0.02 | 0.04 | 0.01 | 0.17 | 0.01 | 0.13 | 0.01 | 0.08 | 0.01 | 0.10 | 0.03 | 0.04 | 0.12 | 0.24 | 0.00 | 0.12 | 0.01 | 0.19 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.70 | 0.01 | 0.25 | 0.03 | 0.13 | 0.01 | 0.12 | 0.03 | 0.56 | 0.00 | 0.22 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.22 | 0.01 |
| ITPKA | ENSG00000137825 | 0.00 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.01 | 0.06 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.37 | 0.01 | 0.10 | 0.01 | 0.09 | 0.02 | 0.05 | 0.03 | 0.06 | 0.00 | 0.09 | 0.01 | 0.09 | 0.00 | 0.06 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.07 | 0.06 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.12 | 0.03 | 0.38 | 0.00 | 0.11 | 0.00 | 0.09 | 0.05 | 0.37 | 0.06 | 0.08 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.15 | 0.01 | 0.02 | 0.01 | 0.12 | 0.00 | 0.00 | 0.01 | 0.19 |
| ATP11A | ENSG00000068650 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.21 | 0.02 | 0.00 | 0.01 | 0.03 | 0.02 | 0.12 | 0.08 | 0.21 | 0.05 | 0.16 | 0.01 | 0.21 | 0.03 | 0.17 | 0.03 | 0.12 | 0.01 | 0.17 | 0.02 | 0.02 | 0.02 | 0.29 | 0.00 | 0.06 | 0.04 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.05 | 0.25 | 0.14 | 0.23 | 0.01 | 0.10 | 0.03 | 0.33 | 0.12 | 0.41 | 0.12 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.12 | 0.04 | 0.02 | 0.05 | 0.02 | 0.05 | 0.00 | 0.07 | 0.07 |
| ACP6 | ENSG00000162836 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.50 | 0.04 | 0.02 | 0.00 | 0.10 | 0.13 | 0.38 | 0.12 | 0.28 | 0.13 | 0.10 | 0.16 | 0.23 | 0.11 | 0.19 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.05 | 0.01 | 0.33 | 0.03 | 0.39 | 0.01 | 0.17 | 0.03 | 0.10 | 0.26 | 0.00 | 0.00 | 0.36 | 0.05 | 0.60 | 0.09 | 0.15 | 0.06 | 0.25 | 0.02 | 0.41 | 0.04 | 0.41 | 0.12 | 0.12 | 0.03 | 0.00 | 0.00 | 0.28 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.03 | 0.17 | 0.05 |
| GPRC5A | ENSG00000013588 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.17 | 0.03 | 0.08 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.09 | 0.09 | 0.02 | 0.05 | 0.03 | 0.05 | 0.04 | 0.03 | 0.09 | 0.01 | 0.04 | 0.01 | 0.09 | 0.02 | 0.06 | 0.01 | 0.06 | 0.14 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.07 | 0.25 | 0.12 | 0.01 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.11 | 0.16 | 0.54 | 0.00 | 0.00 | 0.06 | 0.00 | 0.13 | 0.03 | 0.03 | 0.00 | 0.06 | 0.00 | 0.01 | 0.04 | 0.03 |
| LEPR | ENSG00000116678 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.06 | 0.00 | 0.02 | 0.02 | 0.01 | 0.05 | 0.06 | 0.05 | 0.05 | 0.03 | 0.04 | 0.02 | 0.06 | 0.02 | 0.05 | 0.00 | 0.07 | 0.00 | 0.05 | 0.00 | 0.01 | 0.06 | 0.04 | 0.00 | 0.17 | 0.02 | 0.03 | 0.02 | 0.17 | 0.00 | 0.00 | 0.07 | 0.07 | 0.16 | 0.13 | 0.05 | 0.02 | 0.03 | 0.02 | 0.00 | 0.05 | 0.24 | 0.02 | 0.01 | 0.05 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.07 | 0.03 | 0.05 |
| PIK3C2G | ENSG00000139144 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.08 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.05 | 0.10 | 0.08 | 0.15 | 0.01 | 0.07 | 0.02 | 0.09 | 0.06 | 0.06 | 0.05 | 0.03 | 0.02 | 0.02 | 0.06 | 0.01 | 0.06 | 0.01 | 0.05 | 0.14 | 0.08 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.05 | 0.27 | 0.09 | 0.01 | 0.01 | 0.06 | 0.01 | 0.22 | 0.03 | 0.24 | 0.12 | 0.60 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.06 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.05 | 0.02 |
| CCDC80 | ENSG00000091986 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.14 | 0.03 | 0.05 | 0.01 | 0.09 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.10 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.06 | 0.02 | 0.38 | 0.04 | 0.05 | 0.01 | 0.04 | 0.01 | 0.09 | 0.08 | 0.13 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| UGGT1 | ENSG00000136731 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.06 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.05 | 0.01 | 0.07 | 0.06 | 0.03 | 0.05 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.11 | 0.17 | 0.03 | 0.00 | 0.03 | 0.01 | 0.11 | 0.03 | 0.14 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 |
| EPHA7 | ENSG00000135333 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.37 | 0.02 | 0.09 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.06 | 0.05 | 0.05 | 0.04 | 0.03 | 0.02 | 0.11 | 0.02 | 0.08 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.20 | 0.08 | 0.02 | 0.00 | 0.09 | 0.00 | 0.00 | 0.05 | 0.11 | 0.14 | 0.14 | 0.02 | 0.01 | 0.02 | 0.02 | 0.16 | 0.05 | 0.07 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.22 | 0.01 | 0.01 | 0.00 | 0.04 | 0.03 | 0.03 | 0.01 | 0.05 |
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