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 |
| CALU | ENSG00000128595 | 0.02 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.08 | 0.02 | 0.07 | 0.07 | 0.02 | 0.13 | 0.03 | 0.19 | 0.05 | 0.06 | 0.03 | 0.01 | 0.03 | 0.02 | 0.01 | 0.04 | 0.05 | 0.05 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.35 | 0.04 | 0.04 | 0.07 | 0.06 | 0.05 | 0.11 | 0.14 | 0.13 | 0.02 | 0.03 | 0.03 | 0.00 | 0.06 | 0.02 | 0.11 | 0.11 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.20 | 0.02 |
| LRRC17 | ENSG00000128606 | 0.01 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.05 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.10 | 0.02 | 0.18 | 0.02 | 0.20 | 0.01 | 0.42 | 0.04 | 0.21 | 0.03 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.03 | 0.05 | 0.02 | 0.04 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.04 | 0.24 | 0.07 | 0.05 | 0.02 | 0.04 | 0.03 | 0.09 | 0.07 | 0.08 | 0.05 | 0.08 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.07 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 |
| OPN1SW | ENSG00000128617 | 0.02 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.08 | 0.02 | 0.07 | 0.07 | 0.02 | 0.13 | 0.03 | 0.19 | 0.05 | 0.06 | 0.03 | 0.00 | 0.03 | 0.02 | 0.01 | 0.04 | 0.05 | 0.05 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.36 | 0.03 | 0.04 | 0.07 | 0.06 | 0.05 | 0.11 | 0.14 | 0.12 | 0.03 | 0.03 | 0.03 | 0.00 | 0.06 | 0.02 | 0.11 | 0.11 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.20 | 0.02 |
| TWSG1 | ENSG00000128791 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.01 | 0.03 | 0.02 | 0.01 | 0.02 | 0.05 | 0.05 | 0.06 | 0.02 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.06 | 0.06 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.08 | 0.06 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 |
| DLL4 | ENSG00000128917 | 0.00 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.01 | 0.06 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.37 | 0.02 | 0.11 | 0.01 | 0.09 | 0.02 | 0.05 | 0.04 | 0.06 | 0.01 | 0.08 | 0.02 | 0.09 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.03 | 0.00 | 0.07 | 0.05 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.12 | 0.05 | 0.35 | 0.01 | 0.11 | 0.03 | 0.09 | 0.10 | 0.37 | 0.05 | 0.08 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.02 | 0.01 | 0.11 | 0.00 | 0.00 | 0.01 | 0.18 |
| DUT | ENSG00000128951 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.01 | 0.05 | 0.03 | 0.05 | 0.00 | 0.00 | 0.05 | 0.18 | 0.01 | 0.06 | 0.03 | 0.06 | 0.02 | 0.03 | 0.02 | 0.03 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.09 | 0.05 | 0.24 | 0.00 | 0.10 | 0.00 | 0.07 | 0.08 | 0.26 | 0.08 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.00 | 0.03 | 0.13 |
| ACKR4 | ENSG00000129048 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.17 | 0.02 | 0.13 | 0.00 | 0.16 | 0.05 | 0.06 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.03 | 0.33 | 0.03 | 0.12 | 0.01 | 0.06 | 0.00 | 0.23 | 0.02 | 0.03 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.05 |
| PSMA1 | ENSG00000129084 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.10 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.03 | 0.16 | 0.09 | 0.04 | 0.04 | 0.05 | 0.04 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.04 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.05 | 0.07 | 0.06 | 0.27 | 0.01 | 0.04 | 0.09 | 0.04 | 0.10 | 0.04 | 0.08 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| SPCS3 | ENSG00000129128 | 0.00 | 0.03 | 0.00 | 0.03 | 0.10 | 0.04 | 0.03 | 0.05 | 0.05 | 0.20 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.11 | 0.02 | 0.18 | 0.01 | 0.11 | 0.06 | 0.13 | 0.02 | 0.16 | 0.01 | 0.09 | 0.02 | 0.06 | 0.00 | 0.05 | 0.06 | 0.18 | 0.00 | 0.30 | 0.10 | 0.11 | 0.00 | 0.04 | 0.00 | 0.01 | 0.04 | 0.10 | 0.06 | 0.36 | 0.04 | 0.09 | 0.01 | 0.08 | 0.09 | 0.16 | 0.05 | 0.22 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.09 | 0.01 | 0.10 | 0.01 | 0.08 | 0.00 | 0.00 | 0.04 | 0.07 |
| USP6 | ENSG00000129204 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.03 | 0.02 | 0.03 | 0.03 | 0.04 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.13 | 0.00 | 0.08 | 0.02 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.10 | 0.05 | 0.01 | 0.03 | 0.04 | 0.03 | 0.09 | 0.15 | 0.16 | 0.26 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.04 | 0.03 |
| SHBG | ENSG00000129214 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.26 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.03 | 0.01 | 0.04 | 0.03 | 0.04 | 0.02 | 0.04 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.16 | 0.02 | 0.08 | 0.04 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.08 | 0.10 | 0.04 | 0.00 | 0.04 | 0.04 | 0.03 | 0.09 | 0.16 | 0.05 | 0.60 | 0.00 | 0.02 | 0.02 | 0.02 | 0.00 | 0.13 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.05 |
| AIPL1 | ENSG00000129221 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.06 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.03 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.14 | 0.00 | 0.08 | 0.03 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.06 | 0.11 | 0.04 | 0.01 | 0.03 | 0.03 | 0.03 | 0.06 | 0.15 | 0.11 | 0.29 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.02 | 0.04 |
| CD68 | ENSG00000129226 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.26 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.16 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.08 | 0.10 | 0.04 | 0.00 | 0.04 | 0.04 | 0.03 | 0.09 | 0.16 | 0.09 | 0.57 | 0.00 | 0.02 | 0.02 | 0.02 | 0.00 | 0.13 | 0.00 | 0.01 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.05 |
| PHF20L1 | ENSG00000129292 | 0.02 | 0.00 | 0.02 | 0.00 | 0.11 | 0.00 | 0.07 | 0.03 | 0.20 | 0.03 | 0.02 | 0.00 | 0.10 | 0.02 | 0.29 | 0.01 | 0.34 | 0.00 | 0.29 | 0.00 | 0.47 | 0.01 | 0.21 | 0.01 | 0.18 | 0.01 | 0.22 | 0.01 | 0.16 | 0.00 | 0.39 | 0.01 | 0.25 | 0.01 | 0.10 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.48 | 0.03 | 1.65 | 0.03 | 0.20 | 0.00 | 0.18 | 0.01 | 0.37 | 0.03 | 0.17 | 0.07 | 0.03 | 0.02 | 0.02 | 0.00 | 0.19 | 0.05 | 0.19 | 0.01 | 0.03 | 0.02 | 0.50 | 0.00 | 0.21 | 0.01 |
| KLK14 | ENSG00000129437 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.08 | 0.07 | 0.10 | 0.03 | 0.02 | 0.06 | 0.03 | 0.08 | 0.03 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.13 | 0.03 | 0.10 | 0.30 | 0.07 | 0.07 | 0.05 | 0.06 | 0.22 | 0.13 | 0.02 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.01 | 0.15 | 0.00 | 0.00 | 0.03 | 0.03 |
| SIGLEC9 | ENSG00000129450 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.08 | 0.07 | 0.10 | 0.03 | 0.02 | 0.07 | 0.03 | 0.08 | 0.03 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.13 | 0.03 | 0.10 | 0.31 | 0.07 | 0.07 | 0.04 | 0.05 | 0.22 | 0.13 | 0.02 | 0.19 | 0.00 | 0.04 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.01 | 0.15 | 0.00 | 0.00 | 0.03 | 0.03 |
| KLK10 | ENSG00000129451 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.08 | 0.07 | 0.10 | 0.03 | 0.02 | 0.07 | 0.03 | 0.09 | 0.03 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.04 | 0.05 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.04 | 0.10 | 0.31 | 0.07 | 0.07 | 0.04 | 0.05 | 0.22 | 0.13 | 0.02 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.01 | 0.14 | 0.00 | 0.00 | 0.03 | 0.03 |
| KLK8 | ENSG00000129455 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.08 | 0.07 | 0.10 | 0.03 | 0.02 | 0.07 | 0.03 | 0.09 | 0.03 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.04 | 0.05 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.04 | 0.10 | 0.31 | 0.07 | 0.07 | 0.04 | 0.05 | 0.24 | 0.13 | 0.03 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.01 | 0.14 | 0.00 | 0.00 | 0.03 | 0.03 |
| RIPK3 | ENSG00000129465 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.15 | 0.02 | 0.09 | 0.07 | 0.05 | 0.07 | 0.11 | 0.04 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.06 | 0.01 | 0.03 | 0.09 | 0.01 | 0.00 | 0.02 | 0.26 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.03 | 0.19 | 0.13 | 0.03 | 0.02 | 0.05 | 0.03 | 0.11 | 0.07 | 0.21 | 0.04 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| BCL2L2 | ENSG00000129473 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.07 | 0.01 | 0.00 | 0.00 | 0.02 | 0.19 | 0.03 | 0.16 | 0.07 | 0.05 | 0.07 | 0.12 | 0.05 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.07 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.28 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.11 | 0.03 | 0.26 | 0.12 | 0.08 | 0.02 | 0.05 | 0.03 | 0.06 | 0.07 | 0.23 | 0.03 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
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