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 |
| MAN2B1 | ENSG00000104774 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.01 | 0.00 | 0.08 | 0.01 | 0.00 | 0.05 | 0.09 | 0.05 | 0.05 | 0.03 | 0.10 | 0.05 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.02 | 0.09 | 0.00 | 0.01 | 0.17 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.04 | 0.64 | 0.14 | 0.10 | 0.04 | 0.20 | 0.04 | 0.30 | 0.17 | 0.18 | 0.03 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.02 | 0.00 | 0.02 | 0.03 |
| HTR2A | ENSG00000102468 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.40 | 0.03 | 0.30 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 | 0.07 | 0.01 | 0.12 | 0.02 | 0.14 | 0.06 | 0.09 | 0.11 | 0.04 | 0.10 | 0.03 | 0.13 | 0.02 | 0.01 | 0.01 | 0.00 | 0.28 | 0.00 | 0.11 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.14 | 0.04 | 0.23 | 0.00 | 0.22 | 0.00 | 0.04 | 0.08 | 0.14 | 0.04 | 0.40 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.00 | 0.08 | 0.00 | 0.14 | 0.00 | 0.00 | 0.01 | 0.04 |
| CLCN3 | ENSG00000109572 | 0.00 | 0.03 | 0.00 | 0.02 | 0.06 | 0.02 | 0.04 | 0.03 | 0.05 | 0.14 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.02 | 0.17 | 0.02 | 0.09 | 0.08 | 0.08 | 0.07 | 0.12 | 0.04 | 0.07 | 0.02 | 0.05 | 0.00 | 0.05 | 0.06 | 0.11 | 0.00 | 0.17 | 0.13 | 0.09 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.09 | 0.09 | 0.31 | 0.05 | 0.10 | 0.02 | 0.06 | 0.12 | 0.10 | 0.08 | 0.18 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.09 | 0.00 | 0.12 | 0.00 | 0.07 | 0.00 | 0.00 | 0.05 | 0.05 |
| SLC25A14 | ENSG00000102078 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.05 | 0.01 | 0.03 | 0.02 | 0.09 | 0.02 | 0.09 | 0.02 | 0.05 | 0.01 | 0.10 | 0.02 | 0.12 | 0.01 | 0.03 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.09 | 0.03 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.19 | 0.05 | 0.08 | 0.00 | 0.03 | 0.01 | 0.08 | 0.08 | 0.02 | 0.14 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| GABRB1 | ENSG00000163288 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.04 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.09 | 0.02 | 0.14 | 0.03 | 0.05 | 0.02 | 0.12 | 0.02 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.07 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.15 | 0.03 | 0.01 | 0.02 | 0.02 | 0.01 | 0.10 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.05 | 0.00 | 0.03 | 0.01 |
| TAF15 | ENSG00000270647 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.11 | 0.04 | 0.01 | 0.01 | 0.00 | 0.05 | 0.07 | 0.01 | 0.02 | 0.05 | 0.02 | 0.03 | 0.12 | 0.08 | 0.14 | 0.02 | 0.06 | 0.02 | 0.05 | 0.01 | 0.05 | 0.01 | 0.04 | 0.04 | 0.11 | 0.01 | 0.03 | 0.14 | 0.00 | 0.13 | 0.00 | 0.00 | 0.13 | 0.09 | 0.03 | 0.20 | 0.00 | 0.02 | 0.03 | 0.07 | 0.17 | 0.10 | 0.05 | 0.18 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 |
| ACVR1B | ENSG00000135503 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.11 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.02 | 0.02 | 0.01 | 0.03 | 0.07 | 0.04 | 0.04 | 0.05 | 0.02 | 0.01 | 0.03 | 0.03 | 0.01 | 0.04 | 0.02 | 0.01 | 0.29 | 0.01 | 0.29 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.06 | 0.14 | 0.05 | 0.03 | 0.00 | 0.07 | 0.01 | 0.29 | 0.04 | 0.12 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.03 | 0.06 | 0.05 | 0.00 | 0.00 | 0.05 | 0.06 |
| SOAT2 | ENSG00000167780 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.03 | 0.02 | 0.01 | 0.03 | 0.04 | 0.03 | 0.05 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.03 | 0.02 | 0.01 | 0.09 | 0.01 | 0.16 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.10 | 0.05 | 0.03 | 0.00 | 0.09 | 0.01 | 0.38 | 0.05 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.00 | 0.00 | 0.02 | 0.06 |
| KHDRBS1 | ENSG00000121774 | 0.00 | 0.04 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.07 | 0.00 | 0.01 | 0.11 | 0.07 | 0.05 | 0.04 | 0.04 | 0.06 | 0.04 | 0.05 | 0.07 | 0.08 | 0.04 | 0.07 | 0.02 | 0.10 | 0.01 | 0.13 | 0.01 | 0.03 | 0.00 | 0.19 | 0.00 | 0.70 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.00 | 0.06 | 0.09 | 0.29 | 0.25 | 0.06 | 0.02 | 0.08 | 0.07 | 0.16 | 0.06 | 0.14 | 0.05 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.07 | 0.05 | 0.05 |
| PEPD | ENSG00000124299 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.22 | 0.03 | 0.00 | 0.00 | 0.11 | 0.01 | 0.25 | 0.01 | 0.37 | 0.02 | 0.07 | 0.02 | 0.24 | 0.04 | 0.15 | 0.06 | 0.06 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.02 | 0.13 | 0.03 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.01 | 0.63 | 0.04 | 0.09 | 0.02 | 0.22 | 0.02 | 1.57 | 0.00 | 0.25 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.07 | 0.02 |
| IGF1 | ENSG00000017427 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 | 0.02 | 0.02 | 0.05 | 0.03 | 0.04 | 0.02 | 0.03 | 0.05 | 0.07 | 0.04 | 0.03 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.03 | 0.04 | 0.00 | 0.22 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.07 | 0.08 | 0.21 | 0.01 | 0.01 | 0.01 | 0.03 | 0.02 | 0.11 | 0.27 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.09 |
| ATP1A4 | ENSG00000132681 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.76 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.28 | 0.00 | 0.28 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.13 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.43 | 0.02 | 0.16 | 0.00 | 0.15 | 0.00 | 0.28 | 0.00 | 0.51 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.16 | 0.00 |
| HSD17B3 | ENSG00000130948 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.01 | 0.04 | 0.04 | 0.01 | 0.04 | 0.00 | 0.06 | 0.02 | 0.02 | 0.04 | 0.02 | 0.02 | 0.04 | 0.03 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.15 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.11 | 0.02 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| NLK | ENSG00000087095 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.25 | 0.01 | 0.06 | 0.01 | 0.00 | 0.03 | 0.07 | 0.01 | 0.13 | 0.02 | 0.04 | 0.02 | 0.13 | 0.02 | 0.11 | 0.01 | 0.10 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.05 | 0.00 | 0.07 | 0.01 | 0.02 | 0.05 | 0.00 | 0.14 | 0.00 | 0.00 | 0.28 | 0.03 | 0.15 | 0.06 | 0.02 | 0.03 | 0.11 | 0.03 | 0.11 | 0.05 | 0.09 | 0.14 | 0.00 | 0.01 | 0.00 | 0.02 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| GABRR2 | ENSG00000111886 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.36 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.06 | 0.07 | 0.03 | 0.03 | 0.03 | 0.05 | 0.07 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.11 | 0.13 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.11 | 0.16 | 0.13 | 0.02 | 0.01 | 0.02 | 0.01 | 0.19 | 0.05 | 0.05 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.20 | 0.00 | 0.01 | 0.00 | 0.04 | 0.06 | 0.03 | 0.03 | 0.04 |
| MAN2B2 | ENSG00000013288 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.09 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.03 | 0.04 | 0.03 | 0.03 | 0.06 | 0.03 | 0.07 | 0.06 | 0.05 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.02 | 0.04 | 0.04 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.05 | 0.25 | 0.07 | 0.04 | 0.05 | 0.07 | 0.03 | 0.17 | 0.00 | 0.09 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.06 | 0.04 |
| GRIN2A | ENSG00000183454 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.22 | 0.05 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.02 | 0.06 | 0.04 | 0.05 | 0.01 | 0.06 | 0.04 | 0.06 | 0.04 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.01 | 0.15 | 0.11 | 0.19 | 0.01 | 0.05 | 0.02 | 0.05 | 0.02 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 |
| PLCZ1 | ENSG00000139151 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.08 | 0.08 | 0.15 | 0.01 | 0.06 | 0.02 | 0.09 | 0.05 | 0.06 | 0.05 | 0.03 | 0.02 | 0.05 | 0.04 | 0.01 | 0.07 | 0.01 | 0.05 | 0.14 | 0.08 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.27 | 0.09 | 0.01 | 0.01 | 0.05 | 0.01 | 0.22 | 0.03 | 0.20 | 0.11 | 0.60 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.06 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.04 | 0.01 |
| ATP2B1 | ENSG00000070961 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.05 | 0.03 | 0.03 | 0.01 | 0.03 | 0.04 | 0.07 | 0.03 | 0.04 | 0.00 | 0.02 | 0.03 | 0.06 | 0.00 | 0.08 | 0.02 | 0.02 | 0.00 | 0.13 | 0.06 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.05 | 0.08 | 0.22 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.16 | 0.47 | 0.05 | 0.02 | 0.01 | 0.00 | 0.01 | 0.15 | 0.05 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.08 |
| REG3G | ENSG00000143954 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.13 | 0.02 | 0.05 | 0.02 | 0.08 | 0.04 | 0.03 | 0.03 | 0.01 | 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 | 0.05 | 0.02 | 0.12 | 0.05 | 0.03 | 0.01 | 0.05 | 0.01 | 0.16 | 0.06 | 0.11 | 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 |
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