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 |
| ATG4B | ENSG00000168397 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.10 | 0.02 | 0.04 | 0.00 | 0.32 | 0.00 | 0.01 | 0.00 | 0.07 | 0.05 | 0.05 | 0.03 | 0.20 | 0.02 | 0.18 | 0.04 | 0.18 | 0.03 | 0.10 | 0.02 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.09 | 0.05 | 0.01 | 0.05 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.12 | 0.22 | 0.30 | 0.02 | 0.38 | 0.03 | 0.08 | 0.13 | 0.09 | 0.05 | 0.53 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.04 | 0.04 | 0.05 | 0.01 | 0.14 |
| SFTPD | ENSG00000133661 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.08 | 0.08 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.08 | 0.05 | 0.04 | 0.04 | 0.05 | 0.04 | 0.13 | 0.05 | 0.05 | 0.02 | 0.13 | 0.03 | 0.06 | 0.00 | 0.02 | 0.04 | 0.25 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.14 | 0.04 | 0.27 | 0.15 | 0.03 | 0.02 | 0.11 | 0.05 | 0.48 | 0.03 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 |
| ROR2 | ENSG00000169071 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.04 | 0.00 | 0.01 | 0.01 | 0.05 | 0.01 | 0.04 | 0.04 | 0.02 | 0.03 | 0.00 | 0.08 | 0.01 | 0.03 | 0.04 | 0.03 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.03 | 0.05 | 0.15 | 0.04 | 0.03 | 0.03 | 0.04 | 0.04 | 0.16 | 0.10 | 0.03 | 0.04 | 0.02 | 0.00 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| ABCC1 | ENSG00000103222 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.06 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.03 | 0.05 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.19 | 0.07 | 0.09 | 0.00 | 0.05 | 0.01 | 0.16 | 0.00 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 |
| PHEX | ENSG00000102174 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.10 | 0.04 | 0.03 | 0.02 | 0.09 | 0.07 | 0.04 | 0.02 | 0.00 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.10 | 0.16 | 0.08 | 0.00 | 0.04 | 0.01 | 0.06 | 0.09 | 0.17 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 |
| CPD | ENSG00000108582 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.20 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.08 | 0.01 | 0.04 | 0.03 | 0.02 | 0.02 | 0.13 | 0.02 | 0.17 | 0.01 | 0.05 | 0.01 | 0.07 | 0.01 | 0.02 | 0.02 | 0.06 | 0.01 | 0.08 | 0.01 | 0.03 | 0.05 | 0.01 | 0.19 | 0.00 | 0.00 | 0.20 | 0.06 | 0.03 | 0.15 | 0.01 | 0.02 | 0.07 | 0.06 | 0.08 | 0.08 | 0.03 | 0.19 | 0.00 | 0.03 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.03 | 0.01 | 0.05 |
| CHRNA9 | ENSG00000174343 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.02 | 0.05 | 0.03 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.06 | 0.01 | 0.00 | 0.09 | 0.01 | 0.04 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.08 | 0.08 | 0.00 | 0.02 | 0.03 | 0.03 | 0.10 | 0.07 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 |
| ITGA5 | ENSG00000161638 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.09 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.01 | 0.04 | 0.02 | 0.02 | 0.02 | 0.05 | 0.03 | 0.07 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.15 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.21 | 0.05 | 0.04 | 0.00 | 0.07 | 0.01 | 0.14 | 0.09 | 0.23 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.04 | 0.03 | 0.05 | 0.08 | 0.00 | 0.03 | 0.05 |
| CYP2S1 | ENSG00000167600 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.13 | 0.03 | 0.00 | 0.00 | 0.08 | 0.02 | 0.09 | 0.04 | 0.17 | 0.07 | 0.03 | 0.02 | 0.03 | 0.05 | 0.07 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.07 | 0.02 | 0.03 | 0.03 | 0.12 | 0.01 | 0.07 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.19 | 0.25 | 0.08 | 0.04 | 0.05 | 0.04 | 0.16 | 0.17 | 0.27 | 0.10 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.07 | 0.01 | 0.08 | 0.00 | 0.00 | 0.02 | 0.02 |
| PRKAR1B | ENSG00000188191 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.14 | 0.04 | 0.00 | 0.00 | 0.10 | 0.00 | 0.11 | 0.01 | 0.16 | 0.04 | 0.13 | 0.02 | 0.26 | 0.03 | 0.16 | 0.02 | 0.05 | 0.00 | 0.04 | 0.01 | 0.06 | 0.00 | 0.06 | 0.02 | 0.01 | 0.01 | 0.16 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.14 | 0.41 | 0.05 | 0.02 | 0.05 | 0.08 | 0.18 | 0.05 | 0.16 | 0.06 | 0.15 | 0.01 | 0.00 | 0.01 | 0.12 | 0.00 | 0.01 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.15 | 0.01 |
| AMPD3 | ENSG00000133805 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.01 | 0.02 | 0.09 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.06 | 0.03 | 0.14 | 0.02 | 0.05 | 0.08 | 0.08 | 0.03 | 0.03 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.05 | 0.02 | 0.00 | 0.03 | 0.01 | 0.04 | 0.03 | 0.06 | 0.00 | 0.00 | 0.04 | 0.09 | 0.02 | 0.39 | 0.01 | 0.06 | 0.03 | 0.07 | 0.03 | 0.05 | 0.05 | 0.12 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.04 |
| ADAMTS6 | ENSG00000049192 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.19 | 0.03 | 0.17 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.01 | 0.10 | 0.02 | 0.07 | 0.04 | 0.16 | 0.02 | 0.12 | 0.01 | 0.07 | 0.03 | 0.06 | 0.00 | 0.07 | 0.00 | 0.02 | 0.00 | 0.13 | 0.08 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.03 | 0.64 | 0.00 | 0.09 | 0.03 | 0.12 | 0.04 | 0.38 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 |
| SLC9B2 | ENSG00000164038 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.02 | 0.07 | 0.02 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.13 | 0.00 | 0.03 | 0.04 | 0.09 | 0.04 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.03 | 0.31 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.11 | 0.02 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 |
| GANC | ENSG00000214013 | 0.00 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.01 | 0.06 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.34 | 0.00 | 0.10 | 0.01 | 0.09 | 0.02 | 0.05 | 0.02 | 0.07 | 0.00 | 0.08 | 0.01 | 0.08 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.07 | 0.02 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.11 | 0.04 | 0.36 | 0.00 | 0.10 | 0.01 | 0.09 | 0.05 | 0.44 | 0.06 | 0.08 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.15 | 0.00 | 0.03 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.18 |
| CARD17 | ENSG00000255221 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.03 | 0.01 | 0.07 | 0.08 | 0.09 | 0.00 | 0.00 | 0.02 | 0.08 | 0.06 | 0.07 | 0.07 | 0.08 | 0.07 | 0.14 | 0.17 | 0.07 | 0.03 | 0.06 | 0.02 | 0.03 | 0.02 | 0.03 | 0.01 | 0.02 | 0.02 | 0.06 | 0.00 | 0.14 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.05 | 0.20 | 0.25 | 0.15 | 0.14 | 0.22 | 0.02 | 0.06 | 0.14 | 0.27 | 0.11 | 0.20 | 0.01 | 0.10 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.06 | 0.19 |
| PLA1A | ENSG00000144837 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.11 | 0.02 | 0.03 | 0.00 | 0.07 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.26 | 0.03 | 0.05 | 0.01 | 0.04 | 0.01 | 0.05 | 0.08 | 0.09 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.04 |
| ACACA | ENSG00000278540 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.13 | 0.04 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.00 | 0.05 | 0.05 | 0.05 | 0.03 | 0.13 | 0.07 | 0.25 | 0.01 | 0.11 | 0.02 | 0.05 | 0.03 | 0.07 | 0.01 | 0.04 | 0.05 | 0.12 | 0.01 | 0.04 | 0.11 | 0.00 | 0.13 | 0.00 | 0.00 | 0.20 | 0.10 | 0.06 | 0.17 | 0.01 | 0.02 | 0.10 | 0.07 | 0.10 | 0.17 | 0.10 | 0.13 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.05 | 0.01 | 0.03 |
| CDC14B | ENSG00000081377 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.01 | 0.04 | 0.04 | 0.01 | 0.04 | 0.01 | 0.07 | 0.02 | 0.03 | 0.04 | 0.02 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.04 | 0.16 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.12 | 0.02 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| SLC47A2 | ENSG00000180638 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.15 | 0.06 | 0.00 | 0.01 | 0.00 | 0.02 | 0.08 | 0.04 | 0.09 | 0.04 | 0.03 | 0.03 | 0.07 | 0.08 | 0.04 | 0.05 | 0.02 | 0.03 | 0.01 | 0.07 | 0.08 | 0.01 | 0.09 | 0.04 | 0.09 | 0.01 | 0.10 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.05 | 0.04 | 0.15 | 0.02 | 0.05 | 0.07 | 0.06 | 0.26 | 0.21 | 0.68 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
| AQP9 | ENSG00000103569 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.02 | 0.01 | 0.05 | 0.05 | 0.04 | 0.00 | 0.00 | 0.08 | 0.07 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.02 | 0.03 | 0.02 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.07 | 0.06 | 0.15 | 0.03 | 0.06 | 0.00 | 0.08 | 0.06 | 0.26 | 0.09 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.00 | 0.03 | 0.07 |
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