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 |
| CACNA1A | ENSG00000141837 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.00 | 0.00 | 0.09 | 0.02 | 0.02 | 0.05 | 0.11 | 0.06 | 0.07 | 0.02 | 0.14 | 0.05 | 0.06 | 0.02 | 0.04 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.09 | 0.00 | 0.03 | 0.21 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.88 | 0.09 | 0.11 | 0.03 | 0.29 | 0.02 | 0.29 | 0.13 | 0.24 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 |
| STAMBP | ENSG00000124356 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.13 | 0.01 | 0.05 | 0.00 | 0.07 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.03 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.16 | 0.04 | 0.03 | 0.00 | 0.05 | 0.01 | 0.10 | 0.02 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.04 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| SLC17A1 | ENSG00000124568 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.27 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.07 | 0.02 | 0.07 | 0.06 | 0.02 | 0.05 | 0.10 | 0.11 | 0.04 | 0.04 | 0.04 | 0.03 | 0.04 | 0.03 | 0.03 | 0.03 | 0.11 | 0.01 | 0.06 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.03 | 0.38 | 0.05 | 0.09 | 0.04 | 0.05 | 0.01 | 0.20 | 0.02 | 0.04 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.16 | 0.00 | 0.16 | 0.01 |
| CSK | ENSG00000103653 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.02 | 0.06 | 0.02 | 0.02 | 0.03 | 0.08 | 0.03 | 0.05 | 0.03 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.02 | 0.05 | 0.03 | 0.00 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.16 | 0.15 | 0.12 | 0.01 | 0.04 | 0.04 | 0.14 | 0.07 | 0.05 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.13 | 0.01 |
| PRMT7 | ENSG00000132600 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.08 | 0.16 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.03 | 0.06 | 0.02 | 0.03 | 0.02 | 0.18 | 0.05 | 0.05 | 0.04 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.05 | 0.01 | 0.24 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.05 | 0.05 | 0.03 | 0.33 | 0.03 | 0.02 | 0.03 | 0.09 | 0.02 | 0.14 | 0.02 | 0.05 | 0.15 | 0.02 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 |
| LRRTM3 | ENSG00000198739 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.03 | 0.06 | 0.04 | 0.03 | 0.03 | 0.06 | 0.11 | 0.07 | 0.07 | 0.01 | 0.04 | 0.07 | 0.02 | 0.01 | 0.00 | 0.03 | 0.04 | 0.25 | 0.04 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.11 | 0.14 | 0.00 | 0.02 | 0.04 | 0.06 | 0.11 | 0.15 | 0.01 | 0.14 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 |
| PRSS57 | ENSG00000185198 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.05 | 0.00 | 0.03 | 0.09 | 0.03 | 0.09 | 0.03 | 0.16 | 0.01 | 0.15 | 0.05 | 0.18 | 0.05 | 0.07 | 0.01 | 0.06 | 0.02 | 0.09 | 0.00 | 0.07 | 0.02 | 0.12 | 0.04 | 0.03 | 0.11 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.91 | 0.04 | 0.23 | 0.03 | 0.25 | 0.00 | 0.84 | 0.27 | 0.21 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.08 | 0.01 | 0.08 | 0.01 | 0.01 | 0.03 | 0.02 | 0.08 |
| HIF1A | ENSG00000100644 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.06 | 0.03 | 0.02 | 0.05 | 0.08 | 0.01 | 0.06 | 0.01 | 0.05 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.07 | 0.00 | 0.29 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.05 | 0.07 | 0.06 | 0.25 | 0.02 | 0.01 | 0.01 | 0.02 | 0.10 | 0.04 | 0.04 | 0.10 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.10 | 0.01 | 0.06 | 0.03 | 0.00 | 0.01 | 0.04 |
| RHBDL3 | ENSG00000141314 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.24 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.07 | 0.02 | 0.05 | 0.03 | 0.04 | 0.02 | 0.19 | 0.01 | 0.17 | 0.01 | 0.07 | 0.01 | 0.07 | 0.01 | 0.07 | 0.02 | 0.05 | 0.03 | 0.08 | 0.01 | 0.05 | 0.09 | 0.00 | 0.19 | 0.00 | 0.00 | 0.14 | 0.08 | 0.03 | 0.19 | 0.01 | 0.02 | 0.07 | 0.06 | 0.15 | 0.07 | 0.04 | 0.17 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.03 | 0.02 | 0.03 |
| IL18R1 | ENSG00000115604 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.10 | 0.01 | 0.07 | 0.01 | 0.20 | 0.02 | 0.08 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.16 | 0.07 | 0.03 | 0.01 | 0.05 | 0.01 | 0.09 | 0.00 | 0.13 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| AGTPBP1 | ENSG00000135049 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.02 | 0.01 | 0.06 | 0.01 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.07 | 0.01 | 0.02 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.15 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.13 | 0.00 | 0.03 | 0.03 | 0.03 | 0.00 | 0.15 | 0.15 | 0.00 | 0.03 | 0.02 | 0.00 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| ALPK1 | ENSG00000073331 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.03 | 0.05 | 0.03 | 0.02 | 0.04 | 0.04 | 0.02 | 0.06 | 0.01 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.09 | 0.00 | 0.11 | 0.08 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.05 | 0.27 | 0.01 | 0.02 | 0.01 | 0.05 | 0.00 | 0.11 | 0.05 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.06 |
| CSNK1G2 | ENSG00000133275 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.13 | 0.05 | 0.00 | 0.03 | 0.10 | 0.02 | 0.09 | 0.03 | 0.13 | 0.01 | 0.14 | 0.02 | 0.18 | 0.01 | 0.09 | 0.01 | 0.06 | 0.02 | 0.09 | 0.00 | 0.07 | 0.03 | 0.13 | 0.00 | 0.03 | 0.19 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.92 | 0.07 | 0.19 | 0.01 | 0.27 | 0.04 | 0.77 | 0.19 | 0.16 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.03 | 0.02 | 0.07 | 0.01 | 0.02 | 0.02 | 0.03 | 0.08 |
| HCAR1 | ENSG00000196917 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.02 | 0.03 | 0.05 | 0.08 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.02 | 0.06 | 0.03 | 0.03 | 0.10 | 0.04 | 0.05 | 0.04 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.06 | 0.03 | 0.09 | 0.00 | 0.17 | 0.10 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.13 | 0.24 | 0.02 | 0.02 | 0.04 | 0.07 | 0.17 | 0.22 | 0.12 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.07 |
| GRM1 | ENSG00000152822 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.07 | 0.06 | 0.00 | 0.03 | 0.00 | 0.19 | 0.02 | 0.05 | 0.06 | 0.03 | 0.03 | 0.03 | 0.12 | 0.03 | 0.09 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.03 | 0.01 | 0.10 | 0.00 | 0.18 | 0.18 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.07 | 0.04 | 0.38 | 0.01 | 0.06 | 0.03 | 0.04 | 0.08 | 0.03 | 0.44 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.06 | 0.00 | 0.10 | 0.04 | 0.09 | 0.02 | 0.13 |
| MBNL1 | ENSG00000152601 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.11 | 0.01 | 0.88 | 0.01 | 0.45 | 0.00 | 0.53 | 0.02 | 0.11 | 0.01 | 0.01 | 0.01 | 0.05 | 0.01 | 0.02 | 0.01 | 0.08 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.16 | 0.02 | 0.69 | 0.02 | 0.41 | 0.01 | 0.15 | 0.01 | 0.23 | 0.07 | 0.06 | 0.10 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| GFRA3 | ENSG00000146013 | 0.29 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.03 | 0.01 | 0.03 | 0.03 | 0.03 | 0.02 | 0.04 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.09 | 0.02 | 0.09 | 0.01 | 0.24 | 0.02 | 0.02 | 0.06 | 0.01 | 0.00 | 0.03 | 0.02 | 0.13 | 0.12 | 0.03 | 0.01 | 0.03 | 0.01 | 0.15 | 0.01 | 0.07 | 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 | 0.13 |
| OXSR1 | ENSG00000172939 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.13 | 0.04 | 0.00 | 0.03 | 0.02 | 0.28 | 0.01 | 0.04 | 0.03 | 0.05 | 0.00 | 0.04 | 0.03 | 0.04 | 0.07 | 0.07 | 0.00 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.20 | 0.05 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.08 | 0.11 | 0.16 | 0.02 | 0.04 | 0.03 | 0.04 | 0.12 | 0.15 | 0.09 | 0.06 | 0.03 | 0.04 | 0.00 | 0.01 | 0.06 | 0.09 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.03 | 0.04 | 0.05 |
| MFSD11 | ENSG00000092931 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.19 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.16 | 0.01 | 0.22 | 0.02 | 0.08 | 0.04 | 0.20 | 0.07 | 0.07 | 0.03 | 0.04 | 0.01 | 0.06 | 0.03 | 0.04 | 0.10 | 0.26 | 0.02 | 0.08 | 0.01 | 0.08 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.35 | 0.04 | 0.34 | 0.04 | 0.17 | 0.05 | 0.13 | 0.02 | 0.45 | 0.04 | 0.20 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.04 | 0.01 | 0.12 | 0.03 | 0.25 | 0.02 |
| ADAMTS10 | ENSG00000142303 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.06 | 0.00 | 0.01 | 0.05 | 0.03 | 0.02 | 0.05 | 0.08 | 0.07 | 0.04 | 0.07 | 0.01 | 0.10 | 0.02 | 0.08 | 0.01 | 0.01 | 0.00 | 0.06 | 0.02 | 0.03 | 0.01 | 0.11 | 0.00 | 0.01 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.06 | 0.37 | 0.34 | 0.10 | 0.10 | 0.11 | 0.16 | 0.13 | 0.44 | 0.20 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.02 | 0.02 | 0.03 | 0.02 |
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