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 |
| ICAM3 | ENSG00000076662 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.04 | 0.00 | 0.01 | 0.09 | 0.01 | 0.02 | 0.04 | 0.08 | 0.06 | 0.05 | 0.04 | 0.05 | 0.06 | 0.04 | 0.04 | 0.02 | 0.01 | 0.02 | 0.04 | 0.01 | 0.03 | 0.04 | 0.12 | 0.00 | 0.01 | 0.13 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.04 | 0.60 | 0.20 | 0.12 | 0.06 | 0.21 | 0.08 | 0.74 | 0.18 | 0.27 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.02 | 0.03 | 0.02 |
| ITPR3 | ENSG00000096433 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.05 | 0.00 | 0.01 | 0.03 | 0.02 | 0.07 | 0.01 | 0.03 | 0.06 | 0.02 | 0.04 | 0.15 | 0.06 | 0.06 | 0.04 | 0.03 | 0.01 | 0.06 | 0.02 | 0.04 | 0.02 | 0.07 | 0.01 | 0.05 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.29 | 0.05 | 0.09 | 0.01 | 0.07 | 0.01 | 0.12 | 0.01 | 0.03 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.02 | 0.00 | 0.01 | 0.01 | 0.10 | 0.00 | 0.10 | 0.01 |
| TRIM33 | ENSG00000197323 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.33 | 0.01 | 0.14 | 0.02 | 0.17 | 0.00 | 0.15 | 0.09 | 0.19 | 0.04 | 0.08 | 0.00 | 0.07 | 0.06 | 0.08 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.15 | 0.02 | 0.05 | 0.03 | 0.26 | 0.00 | 0.00 | 0.06 | 0.08 | 0.16 | 0.14 | 0.01 | 0.08 | 0.02 | 0.03 | 0.06 | 0.06 | 0.03 | 0.12 | 0.05 | 0.03 | 0.00 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.13 | 0.10 |
| NTSR2 | ENSG00000169006 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.06 | 0.02 | 0.02 | 0.11 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.05 | 0.02 | 0.09 | 0.04 | 0.02 | 0.04 | 0.05 | 0.07 | 0.05 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.03 | 0.14 | 0.01 | 0.00 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.23 | 0.16 | 0.08 | 0.01 | 0.11 | 0.03 | 0.32 | 0.04 | 0.04 | 0.11 | 0.16 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.03 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.01 | 0.04 |
| CYP2C9 | ENSG00000138109 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.11 | 0.02 | 0.10 | 0.00 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.02 | 0.07 | 0.01 | 0.06 | 0.02 | 0.08 | 0.01 | 0.10 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.03 | 0.01 | 0.06 | 0.16 | 0.07 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.08 | 0.07 | 0.30 | 0.00 | 0.06 | 0.02 | 0.10 | 0.03 | 0.09 | 0.03 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.05 |
| CDK10 | ENSG00000185324 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.06 | 0.01 | 0.23 | 0.08 | 0.06 | 0.00 | 0.00 | 0.02 | 0.19 | 0.01 | 0.12 | 0.04 | 0.07 | 0.03 | 0.05 | 0.08 | 0.05 | 0.05 | 0.05 | 0.02 | 0.03 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.08 | 0.05 | 0.05 | 0.07 | 0.06 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.10 | 0.08 | 0.35 | 0.05 | 0.07 | 0.01 | 0.09 | 0.03 | 0.29 | 0.09 | 0.07 | 0.00 | 0.12 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.06 | 0.02 | 0.11 |
| SPARCL1 | ENSG00000152583 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.13 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.06 | 0.04 | 0.05 | 0.02 | 0.04 | 0.07 | 0.03 | 0.07 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.11 | 0.00 | 0.03 | 0.09 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.22 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.09 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 |
| KLHL3 | ENSG00000146021 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.02 | 0.03 | 0.01 | 0.03 | 0.03 | 0.03 | 0.02 | 0.06 | 0.01 | 0.03 | 0.02 | 0.02 | 0.01 | 0.01 | 0.08 | 0.02 | 0.09 | 0.01 | 0.22 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.02 | 0.12 | 0.12 | 0.03 | 0.02 | 0.02 | 0.01 | 0.10 | 0.01 | 0.10 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.12 |
| CMKLR1 | ENSG00000174600 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.05 | 0.02 | 0.05 | 0.02 | 0.03 | 0.08 | 0.04 | 0.05 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.03 | 0.00 | 0.22 | 0.11 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.07 | 0.09 | 0.21 | 0.02 | 0.01 | 0.01 | 0.05 | 0.07 | 0.09 | 0.18 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.07 |
| CPVL | ENSG00000106066 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.08 | 0.03 | 0.06 | 0.01 | 0.16 | 0.02 | 0.05 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.16 | 0.14 | 0.02 | 0.00 | 0.05 | 0.02 | 0.08 | 0.01 | 0.20 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 |
| IFIT1 | ENSG00000185745 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.22 | 0.03 | 0.12 | 0.00 | 0.02 | 0.01 | 0.12 | 0.01 | 0.04 | 0.02 | 0.10 | 0.01 | 0.07 | 0.02 | 0.13 | 0.00 | 0.11 | 0.01 | 0.08 | 0.00 | 0.08 | 0.01 | 0.02 | 0.03 | 0.06 | 0.20 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.11 | 0.08 | 0.30 | 0.01 | 0.10 | 0.04 | 0.09 | 0.09 | 0.12 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.23 | 0.00 | 0.04 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.04 |
| HSPH1 | ENSG00000120694 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.11 | 0.17 | 0.08 | 0.00 | 0.02 | 0.00 | 0.18 | 0.02 | 0.08 | 0.04 | 0.11 | 0.02 | 0.14 | 0.13 | 0.06 | 0.17 | 0.03 | 0.16 | 0.00 | 0.22 | 0.04 | 0.01 | 0.01 | 0.02 | 0.15 | 0.00 | 0.14 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.08 | 0.06 | 0.19 | 0.03 | 0.16 | 0.00 | 0.05 | 0.01 | 0.15 | 0.10 | 0.30 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.05 | 0.01 | 0.07 | 0.00 | 0.00 | 0.09 | 0.02 |
| PPARD | ENSG00000112033 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.03 | 0.05 | 0.03 | 0.03 | 0.14 | 0.04 | 0.07 | 0.03 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.05 | 0.02 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.26 | 0.05 | 0.08 | 0.01 | 0.04 | 0.01 | 0.36 | 0.05 | 0.12 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.10 | 0.00 | 0.10 | 0.00 |
| FKTN | ENSG00000106692 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.05 | 0.00 | 0.01 | 0.02 | 0.05 | 0.03 | 0.02 | 0.06 | 0.01 | 0.06 | 0.01 | 0.08 | 0.04 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.09 | 0.13 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.10 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| SLC40A1 | ENSG00000138449 | 0.02 | 0.02 | 0.09 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.14 | 0.03 | 0.15 | 0.04 | 0.14 | 0.02 | 0.08 | 0.04 | 0.01 | 0.00 | 0.04 | 0.03 | 0.03 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.45 | 0.04 | 0.12 | 0.02 | 0.07 | 0.01 | 0.00 | 0.03 | 0.07 | 0.09 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 |
| INPP5A | ENSG00000068383 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.10 | 0.01 | 0.03 | 0.02 | 0.11 | 0.04 | 0.06 | 0.05 | 0.07 | 0.03 | 0.04 | 0.06 | 0.09 | 0.08 | 0.08 | 0.02 | 0.06 | 0.02 | 0.05 | 0.01 | 0.01 | 0.02 | 0.10 | 0.14 | 0.17 | 0.11 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.08 | 0.12 | 0.28 | 0.23 | 0.03 | 0.05 | 0.06 | 0.06 | 0.16 | 0.04 | 0.05 | 0.17 | 0.04 | 0.14 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.14 | 0.00 | 0.11 | 0.00 | 0.00 | 0.01 | 0.08 |
| CDC42BPA | ENSG00000143776 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.10 | 0.04 | 0.02 | 0.02 | 0.05 | 0.01 | 0.09 | 0.01 | 0.12 | 0.01 | 0.06 | 0.01 | 0.19 | 0.04 | 0.10 | 0.02 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.14 | 0.03 | 0.23 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.23 | 0.02 | 0.41 | 0.05 | 0.08 | 0.01 | 0.09 | 0.02 | 0.23 | 0.00 | 0.04 | 0.25 | 0.03 | 0.05 | 0.02 | 0.00 | 0.02 | 0.18 | 0.02 | 0.02 | 0.03 | 0.05 | 0.09 | 0.03 | 0.12 | 0.05 |
| ST6GAL1 | ENSG00000073849 | 0.05 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.14 | 0.05 | 1.55 | 0.01 | 0.61 | 0.00 | 0.70 | 0.02 | 0.22 | 0.01 | 0.04 | 0.01 | 0.06 | 0.02 | 0.03 | 0.00 | 0.13 | 0.02 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.19 | 0.03 | 1.04 | 0.05 | 0.62 | 0.00 | 0.33 | 0.01 | 0.75 | 0.09 | 0.12 | 0.09 | 0.24 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.02 | 0.11 | 0.05 | 0.00 | 0.00 | 0.04 | 0.04 |
| TK2 | ENSG00000166548 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.03 | 0.04 | 0.01 | 0.03 | 0.01 | 0.11 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.23 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.04 | 0.28 | 0.02 | 0.04 | 0.03 | 0.07 | 0.05 | 0.14 | 0.03 | 0.06 | 0.15 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.01 |
| PIP4K2B | ENSG00000276293 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.18 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.13 | 0.01 | 0.07 | 0.04 | 0.06 | 0.01 | 0.32 | 0.03 | 0.33 | 0.01 | 0.13 | 0.01 | 0.09 | 0.02 | 0.06 | 0.02 | 0.02 | 0.06 | 0.05 | 0.01 | 0.05 | 0.15 | 0.01 | 0.13 | 0.00 | 0.00 | 0.42 | 0.08 | 0.09 | 0.17 | 0.05 | 0.02 | 0.16 | 0.05 | 0.13 | 0.09 | 0.04 | 0.13 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.05 | 0.02 | 0.03 |
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