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 |
| CAMK2B | ENSG00000058404 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.09 | 0.03 | 0.03 | 0.01 | 0.10 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.11 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.10 | 0.06 | 0.01 | 0.00 | 0.04 | 0.01 | 0.10 | 0.00 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.11 | 0.02 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 |
| SLC2A13 | ENSG00000151229 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 | 0.10 | 0.03 | 0.03 | 0.03 | 0.02 | 0.04 | 0.04 | 0.06 | 0.06 | 0.05 | 0.01 | 0.01 | 0.02 | 0.03 | 0.04 | 0.04 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.18 | 0.03 | 0.04 | 0.00 | 0.05 | 0.00 | 0.20 | 0.05 | 0.19 | 0.10 | 0.09 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.04 | 0.05 | 0.05 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 |
| CAPN13 | ENSG00000162949 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.07 | 0.05 | 0.02 | 0.11 | 0.01 | 0.03 | 0.01 | 0.04 | 0.04 | 0.02 | 0.04 | 0.00 | 0.01 | 0.01 | 0.03 | 0.01 | 0.03 | 0.07 | 0.00 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.22 | 0.06 | 0.09 | 0.00 | 0.08 | 0.01 | 0.21 | 0.00 | 0.08 | 0.05 | 0.14 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.03 | 0.02 |
| MPO | ENSG00000005381 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.17 | 0.02 | 0.02 | 0.00 | 0.11 | 0.00 | 0.10 | 0.01 | 0.14 | 0.02 | 0.04 | 0.03 | 0.15 | 0.05 | 0.05 | 0.03 | 0.04 | 0.01 | 0.07 | 0.04 | 0.01 | 0.15 | 0.16 | 0.00 | 0.12 | 0.01 | 0.14 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.49 | 0.01 | 0.16 | 0.03 | 0.10 | 0.01 | 0.08 | 0.03 | 0.19 | 0.02 | 0.19 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.03 | 0.00 | 0.17 | 0.00 | 0.20 | 0.02 |
| TRPV4 | ENSG00000111199 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.11 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.05 | 0.02 | 0.04 | 0.02 | 0.03 | 0.09 | 0.05 | 0.06 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.06 | 0.04 | 0.04 | 0.00 | 0.22 | 0.03 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.10 | 0.21 | 0.03 | 0.02 | 0.03 | 0.04 | 0.08 | 0.07 | 0.15 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.04 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.07 |
| UMODL1 | ENSG00000177398 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.08 | 0.01 | 0.06 | 0.02 | 0.09 | 0.02 | 0.07 | 0.01 | 0.01 | 0.01 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.07 | 0.03 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.12 | 0.17 | 0.03 | 0.04 | 0.04 | 0.02 | 0.04 | 0.03 | 0.08 | 0.06 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 |
| STK35 | ENSG00000125834 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.13 | 0.01 | 0.03 | 0.03 | 0.08 | 0.04 | 0.04 | 0.02 | 0.05 | 0.04 | 0.06 | 0.10 | 0.01 | 0.03 | 0.05 | 0.01 | 0.00 | 0.03 | 0.01 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.06 | 0.32 | 0.08 | 0.03 | 0.02 | 0.07 | 0.03 | 0.11 | 0.07 | 0.07 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.02 |
| CLCA1 | ENSG00000016490 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.29 | 0.03 | 0.09 | 0.05 | 0.05 | 0.01 | 0.07 | 0.01 | 0.07 | 0.01 | 0.07 | 0.00 | 0.07 | 0.01 | 0.08 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.10 | 0.04 | 0.07 | 0.00 | 0.23 | 0.00 | 0.00 | 0.04 | 0.09 | 0.12 | 0.18 | 0.02 | 0.04 | 0.02 | 0.03 | 0.10 | 0.05 | 0.12 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.04 | 0.03 | 0.03 | 0.02 | 0.10 |
| PARP10 | ENSG00000178685 | 0.02 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.05 | 0.03 | 0.19 | 0.03 | 0.02 | 0.00 | 0.10 | 0.04 | 0.25 | 0.02 | 0.36 | 0.02 | 0.28 | 0.01 | 0.42 | 0.03 | 0.22 | 0.02 | 0.15 | 0.03 | 0.26 | 0.03 | 0.13 | 0.01 | 0.36 | 0.01 | 0.25 | 0.01 | 0.10 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.42 | 0.04 | 1.51 | 0.05 | 0.21 | 0.01 | 0.13 | 0.02 | 0.26 | 0.03 | 0.20 | 0.11 | 0.06 | 0.03 | 0.02 | 0.00 | 0.26 | 0.02 | 0.17 | 0.05 | 0.04 | 0.03 | 0.50 | 0.00 | 0.24 | 0.02 |
| F13B | ENSG00000143278 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.14 | 0.05 | 0.02 | 0.00 | 0.10 | 0.00 | 0.10 | 0.01 | 0.09 | 0.01 | 0.05 | 0.01 | 0.11 | 0.07 | 0.05 | 0.02 | 0.04 | 0.00 | 0.11 | 0.02 | 0.01 | 0.00 | 0.23 | 0.01 | 0.20 | 0.02 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.19 | 0.01 | 0.28 | 0.06 | 0.07 | 0.00 | 0.07 | 0.01 | 0.07 | 0.03 | 0.14 | 0.10 | 0.05 | 0.00 | 0.01 | 0.01 | 0.26 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.17 | 0.02 |
| CD86 | ENSG00000114013 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.11 | 0.01 | 0.03 | 0.00 | 0.06 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 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 | 0.06 | 0.01 | 0.05 | 0.01 | 0.05 | 0.09 | 0.08 | 0.06 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 |
| PLCE1 | ENSG00000138193 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.12 | 0.03 | 0.10 | 0.00 | 0.02 | 0.00 | 0.14 | 0.01 | 0.03 | 0.04 | 0.07 | 0.00 | 0.06 | 0.02 | 0.08 | 0.01 | 0.10 | 0.00 | 0.10 | 0.06 | 0.06 | 0.01 | 0.03 | 0.01 | 0.06 | 0.16 | 0.07 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.08 | 0.08 | 0.30 | 0.00 | 0.06 | 0.02 | 0.11 | 0.03 | 0.09 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 |
| F11R | ENSG00000158769 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.97 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.27 | 0.00 | 0.29 | 0.00 | 0.06 | 0.00 | 0.32 | 0.00 | 0.13 | 0.00 | 0.03 | 0.00 | 0.14 | 0.00 | 0.06 | 0.00 | 0.30 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.34 | 0.00 | 0.37 | 0.02 | 0.18 | 0.00 | 0.15 | 0.00 | 0.41 | 0.00 | 0.48 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| CPB1 | ENSG00000153002 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.11 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.09 | 0.01 | 0.76 | 0.01 | 0.41 | 0.00 | 0.49 | 0.03 | 0.09 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.08 | 0.01 | 0.03 | 0.03 | 0.12 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.14 | 0.02 | 0.66 | 0.02 | 0.39 | 0.01 | 0.13 | 0.01 | 0.24 | 0.02 | 0.06 | 0.07 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| ART4 | ENSG00000111339 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.10 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 | 0.09 | 0.09 | 0.02 | 0.05 | 0.03 | 0.13 | 0.03 | 0.04 | 0.07 | 0.01 | 0.03 | 0.00 | 0.07 | 0.03 | 0.05 | 0.01 | 0.04 | 0.14 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.07 | 0.25 | 0.11 | 0.01 | 0.03 | 0.03 | 0.02 | 0.09 | 0.03 | 0.09 | 0.13 | 0.56 | 0.00 | 0.00 | 0.05 | 0.00 | 0.04 | 0.03 | 0.02 | 0.00 | 0.06 | 0.00 | 0.01 | 0.04 | 0.02 |
| TASP1 | ENSG00000089123 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.03 | 0.10 | 0.01 | 0.06 | 0.04 | 0.04 | 0.04 | 0.03 | 0.02 | 0.05 | 0.04 | 0.11 | 0.08 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 | 0.19 | 0.05 | 0.03 | 0.03 | 0.05 | 0.02 | 0.03 | 0.12 | 0.09 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| VRK2 | ENSG00000028116 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.10 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.04 | 0.01 | 0.34 | 0.00 | 0.04 | 0.01 | 0.10 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.07 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.01 | 0.20 | 0.04 | 0.06 | 0.01 | 0.04 | 0.01 | 0.16 | 0.05 | 0.08 | 0.06 | 0.03 | 0.02 | 0.00 | 0.00 | 0.38 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| LAMP1 | ENSG00000185896 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.21 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.12 | 0.07 | 0.24 | 0.05 | 0.15 | 0.01 | 0.20 | 0.03 | 0.14 | 0.03 | 0.10 | 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 | 0.16 | 0.05 | 0.26 | 0.14 | 0.23 | 0.01 | 0.09 | 0.03 | 0.33 | 0.12 | 0.45 | 0.10 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.12 | 0.04 | 0.02 | 0.08 | 0.02 | 0.08 | 0.00 | 0.09 | 0.07 |
| EFNA1 | ENSG00000169242 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.07 | 0.01 | 0.37 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.37 | 0.00 | 0.26 | 0.00 | 0.06 | 0.00 | 0.20 | 0.00 | 0.15 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.41 | 0.00 | 0.53 | 0.01 | 0.18 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.36 | 0.00 | 0.57 | 0.02 | 0.20 | 0.00 | 0.22 | 0.00 | 0.91 | 0.00 | 0.34 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.20 | 0.00 |
| CAPN1 | ENSG00000014216 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.07 | 0.03 | 0.07 | 0.02 | 0.19 | 0.02 | 0.15 | 0.04 | 0.04 | 0.03 | 0.01 | 0.02 | 0.04 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.09 | 0.19 | 0.04 | 0.10 | 0.01 | 0.09 | 0.03 | 0.22 | 0.06 | 0.09 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.06 |
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