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 |
| COPA | ENSG00000122218 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.74 | 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 | 0.41 | 0.02 | 0.16 | 0.00 | 0.15 | 0.00 | 0.28 | 0.00 | 0.49 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.18 | 0.00 |
| PRDM10 | ENSG00000170325 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.05 | 0.03 | 0.05 | 0.03 | 0.11 | 0.00 | 0.00 | 0.13 | 0.06 | 0.07 | 0.09 | 0.04 | 0.13 | 0.04 | 0.14 | 0.10 | 0.14 | 0.06 | 0.07 | 0.02 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.09 | 0.00 | 0.23 | 0.02 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.20 | 0.27 | 0.18 | 0.05 | 0.31 | 0.05 | 0.08 | 0.18 | 0.17 | 0.06 | 0.23 | 0.00 | 0.28 | 0.04 | 0.00 | 0.17 | 0.00 | 0.05 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.01 | 0.26 |
| PIK3R3 | ENSG00000117461 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.04 | 0.10 | 0.03 | 0.00 | 0.00 | 0.09 | 0.03 | 0.08 | 0.03 | 0.08 | 0.02 | 0.06 | 0.02 | 0.03 | 0.02 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.23 | 0.02 | 0.03 | 0.01 | 0.11 | 0.00 | 0.00 | 0.05 | 0.05 | 0.42 | 0.06 | 0.09 | 0.01 | 0.09 | 0.01 | 0.25 | 0.03 | 0.10 | 0.04 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.07 | 0.02 |
| FBL | ENSG00000105202 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.23 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.16 | 0.03 | 0.46 | 0.05 | 0.07 | 0.01 | 0.09 | 0.03 | 0.09 | 0.02 | 0.07 | 0.01 | 0.01 | 0.01 | 0.22 | 0.00 | 0.07 | 0.02 | 0.12 | 0.01 | 0.11 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.16 | 0.03 | 0.73 | 0.15 | 0.22 | 0.03 | 0.20 | 0.03 | 0.98 | 0.11 | 0.27 | 0.11 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.06 | 0.04 | 0.05 | 0.00 | 0.00 | 0.04 | 0.01 |
| CDH2 | ENSG00000170558 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.08 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.11 | 0.02 | 0.16 | 0.03 | 0.11 | 0.04 | 0.17 | 0.06 | 0.06 | 0.07 | 0.02 | 0.04 | 0.02 | 0.04 | 0.05 | 0.05 | 0.02 | 0.02 | 0.00 | 0.05 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.28 | 0.06 | 0.05 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.11 | 0.05 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 |
| KAT6A | ENSG00000083168 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.11 | 0.27 | 0.05 | 0.00 | 0.00 | 0.02 | 0.00 | 0.20 | 0.03 | 0.45 | 0.03 | 0.14 | 0.03 | 0.43 | 0.06 | 0.09 | 0.04 | 0.18 | 0.02 | 0.18 | 0.03 | 0.03 | 0.00 | 0.07 | 0.05 | 0.00 | 0.02 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.44 | 0.05 | 0.39 | 0.05 | 0.10 | 0.02 | 0.26 | 0.01 | 0.99 | 0.07 | 0.15 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.02 |
| TXNDC5 | ENSG00000239264 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.26 | 0.06 | 0.00 | 0.06 | 0.03 | 0.02 | 0.11 | 0.01 | 0.09 | 0.08 | 0.06 | 0.06 | 0.08 | 0.22 | 0.05 | 0.10 | 0.02 | 0.03 | 0.02 | 0.04 | 0.00 | 0.07 | 0.15 | 0.02 | 0.06 | 0.06 | 0.06 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.14 | 0.06 | 0.47 | 0.09 | 0.08 | 0.06 | 0.07 | 0.02 | 0.19 | 0.05 | 0.07 | 0.14 | 0.04 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.02 | 0.03 | 0.01 | 0.03 | 0.19 | 0.00 | 0.24 | 0.01 |
| SIK3 | ENSG00000160584 | 0.00 | 0.02 | 0.00 | 0.06 | 0.02 | 0.02 | 0.01 | 0.09 | 0.03 | 0.11 | 0.00 | 0.00 | 0.02 | 0.07 | 0.05 | 0.08 | 0.04 | 0.10 | 0.04 | 0.16 | 0.08 | 0.13 | 0.06 | 0.08 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.10 | 0.00 | 0.17 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.24 | 0.14 | 0.17 | 0.04 | 0.29 | 0.04 | 0.05 | 0.12 | 0.18 | 0.02 | 0.23 | 0.01 | 0.14 | 0.02 | 0.01 | 0.11 | 0.01 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.07 | 0.00 | 0.27 |
| NUP153 | ENSG00000124789 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.44 | 0.04 | 0.00 | 0.01 | 0.03 | 0.02 | 0.06 | 0.01 | 0.11 | 0.06 | 0.04 | 0.05 | 0.10 | 0.16 | 0.06 | 0.07 | 0.02 | 0.03 | 0.02 | 0.03 | 0.02 | 0.06 | 0.15 | 0.01 | 0.06 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.17 | 0.03 | 0.53 | 0.05 | 0.10 | 0.05 | 0.07 | 0.02 | 0.23 | 0.02 | 0.04 | 0.13 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.21 | 0.00 |
| AHCY | ENSG00000101444 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.20 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.02 | 0.17 | 0.01 | 0.22 | 0.00 | 0.10 | 0.00 | 0.04 | 0.01 | 0.11 | 0.00 | 0.20 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.17 | 0.03 | 0.15 | 0.00 | 0.10 | 0.01 | 0.35 | 0.00 | 0.13 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 |
| IGFBP3 | ENSG00000146674 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.09 | 0.02 | 0.07 | 0.01 | 0.11 | 0.03 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.09 | 0.06 | 0.02 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| ULBP2 | ENSG00000131015 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.04 | 0.08 | 0.00 | 0.03 | 0.00 | 0.17 | 0.01 | 0.06 | 0.05 | 0.05 | 0.03 | 0.04 | 0.08 | 0.05 | 0.09 | 0.05 | 0.02 | 0.01 | 0.04 | 0.03 | 0.00 | 0.04 | 0.01 | 0.11 | 0.00 | 0.16 | 0.11 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.07 | 0.03 | 0.41 | 0.02 | 0.07 | 0.02 | 0.04 | 0.08 | 0.03 | 0.33 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.09 | 0.03 | 0.06 | 0.02 | 0.13 |
| CTSB | ENSG00000164733 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.16 | 0.02 | 0.14 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.07 | 0.01 | 0.10 | 0.00 | 0.08 | 0.54 | 0.04 | 0.43 | 0.02 | 0.01 | 0.10 | 0.00 | 0.15 | 0.06 | 0.05 | 0.01 | 0.11 | 0.00 | 0.01 | 0.06 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.16 | 0.04 | 0.42 | 0.01 | 0.04 | 0.00 | 0.09 | 0.07 | 0.24 | 0.06 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 | 0.03 |
| CHGB | ENSG00000089199 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.04 | 0.12 | 0.01 | 0.05 | 0.02 | 0.08 | 0.01 | 0.06 | 0.01 | 0.04 | 0.04 | 0.05 | 0.09 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.04 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.26 | 0.07 | 0.08 | 0.01 | 0.07 | 0.02 | 0.11 | 0.06 | 0.07 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 |
| STAT5B | ENSG00000173757 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.03 | 0.01 | 0.19 | 0.04 | 0.14 | 0.03 | 0.05 | 0.01 | 0.04 | 0.02 | 0.03 | 0.03 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.14 | 0.00 | 0.12 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.16 | 0.04 | 0.04 | 0.03 | 0.07 | 0.00 | 0.20 | 0.05 | 0.11 | 0.01 | 0.01 | 0.00 | 0.02 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 |
| ALDOA | ENSG00000149925 | 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 | 0.09 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.05 | 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 | 0.08 | 0.01 | 0.12 | 0.03 | 0.02 | 0.02 | 0.10 | 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 |
| MMP10 | ENSG00000166670 | 0.01 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.28 | 0.06 | 0.00 | 0.01 | 0.06 | 0.06 | 0.11 | 0.05 | 0.11 | 0.07 | 0.38 | 0.10 | 0.20 | 0.08 | 0.07 | 0.05 | 0.02 | 0.01 | 0.02 | 0.04 | 0.05 | 0.01 | 0.05 | 0.06 | 0.00 | 0.10 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.06 | 0.19 | 0.36 | 0.13 | 0.74 | 0.11 | 0.06 | 0.05 | 0.10 | 0.25 | 0.22 | 0.15 | 0.01 | 0.08 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.12 | 0.13 |
| PSMC2 | ENSG00000161057 | 0.01 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.02 | 0.19 | 0.02 | 0.20 | 0.01 | 0.44 | 0.04 | 0.17 | 0.03 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.06 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.26 | 0.06 | 0.04 | 0.02 | 0.05 | 0.03 | 0.09 | 0.05 | 0.08 | 0.04 | 0.08 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.07 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 |
| ABCC11 | ENSG00000121270 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.08 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.08 | 0.03 | 0.05 | 0.02 | 0.04 | 0.04 | 0.11 | 0.02 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.08 | 0.08 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.05 | 0.10 | 0.12 | 0.01 | 0.07 | 0.03 | 0.05 | 0.02 | 0.14 | 0.04 | 0.13 | 0.08 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 | 0.06 |
| MELK | ENSG00000165304 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.12 | 0.04 | 0.00 | 0.01 | 0.01 | 0.09 | 0.04 | 0.06 | 0.33 | 0.05 | 0.16 | 0.05 | 0.21 | 0.05 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.19 | 0.05 | 0.13 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.11 | 0.06 | 0.02 | 0.01 | 0.03 | 0.02 | 0.03 | 0.11 | 0.13 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.06 | 0.00 | 0.03 | 0.08 | 0.05 |
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