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 |
| OR6Y1 | ENSG00000197532 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.36 | 0.02 | 0.02 | 0.00 | 0.08 | 0.00 | 0.25 | 0.00 | 0.24 | 0.00 | 0.06 | 0.00 | 0.24 | 0.02 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.28 | 0.00 | 0.35 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.21 | 0.01 | 0.38 | 0.02 | 0.15 | 0.00 | 0.13 | 0.00 | 0.27 | 0.00 | 0.37 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.19 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 |
| GZMM | ENSG00000197540 | 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 | 0.15 | 0.01 | 0.15 | 0.05 | 0.18 | 0.03 | 0.07 | 0.01 | 0.06 | 0.02 | 0.09 | 0.01 | 0.07 | 0.03 | 0.13 | 0.04 | 0.03 | 0.12 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.91 | 0.05 | 0.22 | 0.03 | 0.25 | 0.00 | 0.84 | 0.25 | 0.23 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.05 | 0.02 | 0.08 | 0.01 | 0.01 | 0.03 | 0.03 | 0.08 |
| ELANE | ENSG00000197561 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.14 | 0.05 | 0.00 | 0.03 | 0.10 | 0.04 | 0.09 | 0.03 | 0.16 | 0.01 | 0.15 | 0.04 | 0.18 | 0.05 | 0.08 | 0.01 | 0.06 | 0.02 | 0.09 | 0.00 | 0.07 | 0.02 | 0.14 | 0.04 | 0.03 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.92 | 0.04 | 0.24 | 0.03 | 0.25 | 0.00 | 0.81 | 0.28 | 0.21 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.08 | 0.01 | 0.08 | 0.01 | 0.01 | 0.04 | 0.02 | 0.08 |
| COL4A6 | ENSG00000197565 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 | 0.01 | 0.20 | 0.14 | 0.04 | 0.02 | 0.11 | 0.03 | 0.05 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.09 | 0.06 | 0.05 | 0.03 | 0.02 | 0.02 | 0.04 | 0.02 | 0.08 | 0.17 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| OR11L1 | ENSG00000197591 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.04 | 0.14 | 0.04 | 0.02 | 0.02 | 0.08 | 0.05 | 0.13 | 0.01 | 0.17 | 0.03 | 0.10 | 0.02 | 0.27 | 0.04 | 0.13 | 0.01 | 0.04 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.20 | 0.02 | 0.23 | 0.02 | 0.10 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.29 | 0.02 | 0.48 | 0.12 | 0.13 | 0.01 | 0.12 | 0.02 | 0.32 | 0.00 | 0.09 | 0.24 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.24 | 0.02 |
| ENPP1 | ENSG00000197594 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.13 | 0.02 | 0.04 | 0.06 | 0.03 | 0.04 | 0.02 | 0.10 | 0.02 | 0.06 | 0.04 | 0.02 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.02 | 0.09 | 0.00 | 0.10 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.12 | 0.04 | 0.08 | 0.28 | 0.01 | 0.02 | 0.06 | 0.02 | 0.08 | 0.03 | 0.26 | 0.06 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.05 | 0.01 | 0.12 |
| MFAP5 | ENSG00000197614 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.10 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.08 | 0.13 | 0.01 | 0.11 | 0.02 | 0.07 | 0.02 | 0.06 | 0.08 | 0.02 | 0.02 | 0.03 | 0.03 | 0.00 | 0.07 | 0.01 | 0.05 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.05 | 0.31 | 0.09 | 0.03 | 0.02 | 0.03 | 0.03 | 0.02 | 0.03 | 0.20 | 0.11 | 0.57 | 0.00 | 0.00 | 0.01 | 0.00 | 0.08 | 0.12 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.04 |
| SERPINB2 | ENSG00000197632 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.09 | 0.05 | 0.06 | 0.02 | 0.15 | 0.06 | 0.19 | 0.02 | 0.16 | 0.00 | 0.12 | 0.01 | 0.12 | 0.01 | 0.08 | 0.03 | 0.06 | 0.00 | 0.10 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.07 | 0.34 | 0.02 | 0.03 | 0.00 | 0.07 | 0.01 | 0.11 | 0.09 | 0.07 | 0.00 | 0.07 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 |
| SERPINB13 | ENSG00000197641 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.09 | 0.05 | 0.06 | 0.02 | 0.14 | 0.05 | 0.20 | 0.02 | 0.16 | 0.00 | 0.12 | 0.01 | 0.11 | 0.00 | 0.08 | 0.02 | 0.06 | 0.00 | 0.10 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.05 | 0.09 | 0.33 | 0.03 | 0.03 | 0.01 | 0.07 | 0.01 | 0.09 | 0.13 | 0.07 | 0.00 | 0.07 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 |
| SLC22A24 | ENSG00000197658 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.02 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.12 | 0.01 | 0.05 | 0.02 | 0.06 | 0.01 | 0.13 | 0.03 | 0.14 | 0.04 | 0.03 | 0.02 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.07 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.07 | 0.15 | 0.04 | 0.07 | 0.01 | 0.07 | 0.02 | 0.29 | 0.12 | 0.07 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 |
| OR51C1P | ENSG00000197674 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.10 | 0.00 | 0.00 | 0.03 | 0.05 | 0.02 | 0.06 | 0.02 | 0.14 | 0.01 | 0.07 | 0.02 | 0.10 | 0.03 | 0.05 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.07 | 0.03 | 0.07 | 0.00 | 0.00 | 0.02 | 0.11 | 0.02 | 0.44 | 0.01 | 0.05 | 0.03 | 0.06 | 0.03 | 0.09 | 0.04 | 0.14 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.10 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.03 |
| NMB | ENSG00000197696 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.03 | 0.00 | 0.11 | 0.00 | 0.04 | 0.02 | 0.13 | 0.01 | 0.04 | 0.02 | 0.12 | 0.03 | 0.12 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.06 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.24 | 0.09 | 0.16 | 0.00 | 0.03 | 0.03 | 0.27 | 0.05 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.01 |
| OR6C74 | ENSG00000197706 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.06 | 0.03 | 0.08 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.08 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.14 | 0.04 | 0.06 | 0.00 | 0.05 | 0.01 | 0.12 | 0.09 | 0.32 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.04 | 0.05 | 0.08 | 0.00 | 0.06 | 0.03 |
| SCGB1D4 | ENSG00000197745 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 | 0.05 | 0.02 | 0.05 | 0.02 | 0.14 | 0.02 | 0.13 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.02 | 0.04 | 0.02 | 0.10 | 0.07 | 0.08 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.17 | 0.04 | 0.06 | 0.00 | 0.10 | 0.01 | 0.27 | 0.12 | 0.07 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 |
| TXNRD3 | ENSG00000197763 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.11 | 0.02 | 0.05 | 0.00 | 0.10 | 0.04 | 0.06 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.03 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.23 | 0.04 | 0.08 | 0.00 | 0.05 | 0.00 | 0.09 | 0.07 | 0.06 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 |
| CFD | ENSG00000197766 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.14 | 0.05 | 0.00 | 0.03 | 0.10 | 0.04 | 0.09 | 0.03 | 0.16 | 0.01 | 0.15 | 0.04 | 0.18 | 0.05 | 0.08 | 0.01 | 0.06 | 0.02 | 0.09 | 0.00 | 0.07 | 0.02 | 0.14 | 0.04 | 0.03 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.92 | 0.04 | 0.24 | 0.03 | 0.25 | 0.00 | 0.81 | 0.28 | 0.21 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.08 | 0.01 | 0.08 | 0.01 | 0.01 | 0.04 | 0.02 | 0.08 |
| OR5B17 | ENSG00000197786 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.02 | 0.14 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.04 | 0.04 | 0.07 | 0.02 | 0.11 | 0.02 | 0.14 | 0.05 | 0.00 | 0.04 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.07 | 0.06 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.10 | 0.07 | 0.12 | 0.05 | 0.05 | 0.02 | 0.06 | 0.01 | 0.16 | 0.13 | 0.06 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.10 | 0.02 |
| OR52M1 | ENSG00000197790 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.05 | 0.02 | 0.06 | 0.02 | 0.14 | 0.01 | 0.07 | 0.02 | 0.10 | 0.03 | 0.05 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.07 | 0.03 | 0.07 | 0.00 | 0.00 | 0.02 | 0.11 | 0.02 | 0.44 | 0.01 | 0.05 | 0.02 | 0.06 | 0.03 | 0.09 | 0.05 | 0.14 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.10 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.03 |
| HIST4H4 | ENSG00000197837 | 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 | 0.01 | 0.05 | 0.03 | 0.13 | 0.03 | 0.04 | 0.07 | 0.01 | 0.03 | 0.00 | 0.07 | 0.02 | 0.06 | 0.01 | 0.04 | 0.14 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.07 | 0.24 | 0.11 | 0.01 | 0.03 | 0.03 | 0.02 | 0.09 | 0.03 | 0.14 | 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 |
| CYP2A13 | ENSG00000197838 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.15 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.09 | 0.03 | 0.23 | 0.07 | 0.03 | 0.02 | 0.03 | 0.05 | 0.07 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.08 | 0.02 | 0.05 | 0.02 | 0.12 | 0.01 | 0.07 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.21 | 0.25 | 0.08 | 0.04 | 0.06 | 0.04 | 0.26 | 0.17 | 0.25 | 0.11 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.07 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.02 |
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