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 |
| OR1J1 | ENSG00000136834 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.05 | 0.02 | 0.06 | 0.01 | 0.10 | 0.01 | 0.08 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.10 | 0.15 | 0.02 | 0.01 | 0.01 | 0.03 | 0.03 | 0.16 | 0.09 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| OR13C9 | ENSG00000136839 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.04 | 0.05 | 0.00 | 0.01 | 0.02 | 0.05 | 0.02 | 0.02 | 0.06 | 0.00 | 0.05 | 0.00 | 0.08 | 0.01 | 0.03 | 0.03 | 0.00 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.08 | 0.12 | 0.03 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.12 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| ANGPTL2 | ENSG00000136859 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.02 | 0.06 | 0.02 | 0.05 | 0.01 | 0.11 | 0.03 | 0.08 | 0.01 | 0.01 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.03 | 0.03 | 0.07 | 0.04 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.11 | 0.17 | 0.03 | 0.02 | 0.04 | 0.04 | 0.06 | 0.11 | 0.06 | 0.07 | 0.01 | 0.08 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| SLC31A2 | ENSG00000136867 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.04 | 0.01 | 0.05 | 0.00 | 0.11 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.03 | 0.05 | 0.06 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.12 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.15 | 0.11 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| SLC31A1 | ENSG00000136868 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.04 | 0.01 | 0.05 | 0.00 | 0.11 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.03 | 0.05 | 0.06 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.12 | 0.01 | 0.01 | 0.03 | 0.04 | 0.00 | 0.15 | 0.08 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| PRPF4 | ENSG00000136875 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.04 | 0.01 | 0.05 | 0.00 | 0.11 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.03 | 0.05 | 0.06 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.12 | 0.01 | 0.01 | 0.03 | 0.04 | 0.00 | 0.15 | 0.08 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| ATP6V1G1 | ENSG00000136888 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.05 | 0.01 | 0.05 | 0.00 | 0.13 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.03 | 0.05 | 0.06 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.11 | 0.04 | 0.00 | 0.01 | 0.04 | 0.00 | 0.15 | 0.08 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| TSTD2 | ENSG00000136925 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.02 | 0.03 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.04 | 0.05 | 0.01 | 0.04 | 0.00 | 0.07 | 0.02 | 0.02 | 0.04 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.08 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.15 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.08 | 0.04 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| OR1L4 | ENSG00000136939 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.05 | 0.02 | 0.06 | 0.01 | 0.11 | 0.01 | 0.08 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.11 | 0.15 | 0.02 | 0.01 | 0.02 | 0.03 | 0.03 | 0.16 | 0.09 | 0.04 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| CTSV | ENSG00000136943 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.01 | 0.04 | 0.04 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.03 | 0.04 | 0.02 | 0.01 | 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 | 0.05 | 0.15 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.12 | 0.03 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| NOV | ENSG00000136999 | 0.02 | 0.00 | 0.01 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.23 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.22 | 0.01 | 0.32 | 0.01 | 0.24 | 0.00 | 0.47 | 0.01 | 0.27 | 0.00 | 0.15 | 0.00 | 0.26 | 0.00 | 0.10 | 0.00 | 0.38 | 0.01 | 0.25 | 0.01 | 0.14 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.54 | 0.02 | 1.24 | 0.05 | 0.17 | 0.00 | 0.16 | 0.00 | 0.30 | 0.00 | 0.18 | 0.06 | 0.03 | 0.02 | 0.02 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.02 | 0.01 | 0.53 | 0.00 | 0.17 | 0.01 |
| IL33 | ENSG00000137033 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.06 | 0.15 | 0.13 | 0.01 | 0.01 | 0.04 | 0.06 | 0.05 | 0.14 | 0.14 | 0.11 | 0.22 | 0.06 | 0.16 | 0.13 | 0.09 | 0.11 | 0.01 | 0.03 | 0.05 | 0.04 | 0.00 | 0.10 | 0.05 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.10 | 0.06 | 0.16 | 0.19 | 0.21 | 0.04 | 0.06 | 0.03 | 0.02 | 0.17 | 0.24 | 0.13 | 0.01 | 0.09 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.10 | 0.01 | 0.20 | 0.00 | 0.00 | 0.04 | 0.12 |
| CCL21 | ENSG00000137077 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.05 | 0.02 | 0.36 | 0.04 | 0.22 | 0.02 | 0.26 | 0.01 | 0.16 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.02 | 0.01 | 0.24 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.11 | 0.06 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.05 | 0.11 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.06 | 0.00 | 0.00 | 0.06 | 0.05 |
| SIT1 | ENSG00000137078 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.03 | 0.00 | 0.00 | 0.01 | 0.09 | 0.06 | 0.02 | 0.38 | 0.04 | 0.31 | 0.03 | 0.33 | 0.02 | 0.17 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.20 | 0.00 | 0.03 | 0.02 | 0.19 | 0.01 | 0.16 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.12 | 0.06 | 0.02 | 0.01 | 0.06 | 0.01 | 0.00 | 0.13 | 0.14 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.06 | 0.00 | 0.03 | 0.08 | 0.05 |
| IFNA21 | ENSG00000137080 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.06 | 0.01 | 0.03 | 0.10 | 0.39 | 0.00 | 0.04 | 0.00 | 0.71 | 0.03 | 0.26 | 0.05 | 0.34 | 0.06 | 0.15 | 0.02 | 0.29 | 0.01 | 0.18 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.31 | 0.01 | 0.10 | 0.00 | 0.16 | 0.00 | 0.13 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.08 | 0.07 | 0.17 | 0.06 | 0.05 | 0.05 | 0.02 | 0.04 | 0.05 | 0.06 | 0.25 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.23 | 0.01 | 0.98 | 0.00 | 0.00 | 0.01 | 0.29 |
| CD72 | ENSG00000137101 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.03 | 0.00 | 0.00 | 0.01 | 0.09 | 0.07 | 0.02 | 0.38 | 0.04 | 0.30 | 0.03 | 0.35 | 0.02 | 0.17 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.20 | 0.00 | 0.03 | 0.02 | 0.19 | 0.01 | 0.16 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.12 | 0.06 | 0.02 | 0.01 | 0.06 | 0.01 | 0.00 | 0.13 | 0.14 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.06 | 0.00 | 0.03 | 0.08 | 0.05 |
| ALDH1B1 | ENSG00000137124 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.05 | 0.00 | 0.01 | 0.01 | 0.09 | 0.05 | 0.08 | 0.18 | 0.07 | 0.08 | 0.09 | 0.20 | 0.04 | 0.09 | 0.04 | 0.01 | 0.01 | 0.05 | 0.01 | 0.05 | 0.01 | 0.03 | 0.03 | 0.19 | 0.05 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.11 | 0.07 | 0.02 | 0.01 | 0.02 | 0.03 | 0.01 | 0.11 | 0.09 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.07 | 0.00 | 0.03 | 0.07 | 0.07 |
| IGFBPL1 | ENSG00000137142 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.05 | 0.00 | 0.01 | 0.01 | 0.09 | 0.04 | 0.08 | 0.18 | 0.07 | 0.08 | 0.09 | 0.20 | 0.05 | 0.08 | 0.04 | 0.01 | 0.01 | 0.05 | 0.01 | 0.05 | 0.01 | 0.03 | 0.03 | 0.19 | 0.05 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.12 | 0.07 | 0.02 | 0.01 | 0.02 | 0.03 | 0.01 | 0.11 | 0.10 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.07 | 0.00 | 0.03 | 0.08 | 0.07 |
| PPIL1 | ENSG00000137168 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.01 | 0.06 | 0.04 | 0.02 | 0.03 | 0.17 | 0.03 | 0.08 | 0.03 | 0.04 | 0.01 | 0.06 | 0.01 | 0.01 | 0.01 | 0.05 | 0.03 | 0.05 | 0.03 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.33 | 0.04 | 0.08 | 0.00 | 0.07 | 0.01 | 0.34 | 0.03 | 0.06 | 0.07 | 0.05 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.10 | 0.00 | 0.10 | 0.01 |
| PIM1 | ENSG00000137193 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.01 | 0.08 | 0.04 | 0.02 | 0.03 | 0.19 | 0.03 | 0.12 | 0.03 | 0.04 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.07 | 0.02 | 0.05 | 0.03 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.36 | 0.04 | 0.08 | 0.00 | 0.07 | 0.01 | 0.26 | 0.03 | 0.10 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.10 | 0.00 | 0.10 | 0.01 |
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