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 |
| MMP25 | ENSG00000008516 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.17 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.03 | 0.05 | 0.09 | 0.04 | 0.03 | 0.03 | 0.08 | 0.03 | 0.08 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.02 | 0.03 | 0.02 | 0.05 | 0.05 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.09 | 0.19 | 0.10 | 0.02 | 0.05 | 0.05 | 0.08 | 0.05 | 0.09 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 |
| SCP2 | ENSG00000116171 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.06 | 0.10 | 0.04 | 0.00 | 0.00 | 0.06 | 0.04 | 0.08 | 0.05 | 0.06 | 0.03 | 0.04 | 0.03 | 0.04 | 0.03 | 0.03 | 0.04 | 0.01 | 0.04 | 0.02 | 0.04 | 0.01 | 0.01 | 0.03 | 0.06 | 0.00 | 0.25 | 0.02 | 0.03 | 0.00 | 0.17 | 0.00 | 0.00 | 0.07 | 0.04 | 0.29 | 0.10 | 0.08 | 0.02 | 0.05 | 0.02 | 0.04 | 0.04 | 0.21 | 0.04 | 0.07 | 0.04 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.07 | 0.04 | 0.03 |
| CCRL2 | ENSG00000121797 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.00 | 0.03 | 0.07 | 0.10 | 0.00 | 0.04 | 0.00 | 0.52 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.05 | 0.01 | 0.07 | 0.02 | 0.10 | 0.00 | 0.04 | 0.03 | 0.06 | 0.00 | 0.04 | 0.02 | 0.04 | 0.00 | 0.24 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.07 | 0.18 | 0.01 | 0.05 | 0.02 | 0.05 | 0.03 | 0.18 | 0.05 | 0.12 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.05 |
| SCN8A | ENSG00000196876 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.11 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.02 | 0.02 | 0.01 | 0.03 | 0.10 | 0.04 | 0.05 | 0.05 | 0.02 | 0.01 | 0.03 | 0.03 | 0.01 | 0.04 | 0.02 | 0.01 | 0.09 | 0.01 | 0.31 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.06 | 0.12 | 0.05 | 0.03 | 0.00 | 0.05 | 0.01 | 0.20 | 0.04 | 0.18 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.03 | 0.06 | 0.05 | 0.00 | 0.00 | 0.05 | 0.07 |
| P4HA1 | ENSG00000122884 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.04 | 0.06 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.08 | 0.03 | 0.04 | 0.03 | 0.05 | 0.04 | 0.17 | 0.04 | 0.02 | 0.03 | 0.09 | 0.03 | 0.02 | 0.00 | 0.04 | 0.02 | 0.25 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.03 | 0.17 | 0.11 | 0.01 | 0.01 | 0.09 | 0.03 | 0.15 | 0.04 | 0.06 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| RPS6KA6 | ENSG00000072133 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.06 | 0.02 | 0.04 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.04 | 0.02 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.18 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 |
| ADCK3 | ENSG00000163050 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.10 | 0.04 | 0.02 | 0.02 | 0.05 | 0.01 | 0.08 | 0.01 | 0.12 | 0.01 | 0.06 | 0.01 | 0.19 | 0.04 | 0.10 | 0.02 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.14 | 0.03 | 0.18 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.23 | 0.02 | 0.40 | 0.05 | 0.08 | 0.01 | 0.09 | 0.02 | 0.23 | 0.00 | 0.03 | 0.25 | 0.03 | 0.05 | 0.02 | 0.00 | 0.02 | 0.18 | 0.02 | 0.02 | 0.03 | 0.05 | 0.09 | 0.03 | 0.11 | 0.05 |
| SIRT3 | ENSG00000142082 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.05 | 0.03 | 0.08 | 0.02 | 0.16 | 0.03 | 0.08 | 0.02 | 0.15 | 0.04 | 0.07 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.06 | 0.07 | 0.03 | 0.03 | 0.01 | 0.04 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.14 | 0.06 | 0.50 | 0.01 | 0.07 | 0.06 | 0.10 | 0.11 | 0.18 | 0.03 | 0.26 | 0.02 | 0.07 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.11 | 0.03 | 0.07 | 0.00 | 0.00 | 0.02 | 0.03 |
| CTSH | ENSG00000103811 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.04 | 0.00 | 0.00 | 0.08 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.03 | 0.03 | 0.07 | 0.03 | 0.07 | 0.03 | 0.03 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.05 | 0.03 | 0.05 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.19 | 0.11 | 0.12 | 0.01 | 0.03 | 0.03 | 0.13 | 0.05 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.01 |
| TCN2 | ENSG00000185339 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.23 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.02 | 0.18 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.29 | 0.05 | 0.04 | 0.00 | 0.13 | 0.01 | 0.14 | 0.02 | 0.04 | 0.03 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.04 | 0.05 |
| BMPER | ENSG00000164619 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.08 | 0.03 | 0.04 | 0.01 | 0.13 | 0.01 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.14 | 0.09 | 0.01 | 0.00 | 0.05 | 0.02 | 0.08 | 0.00 | 0.13 | 0.03 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 |
| CD37 | ENSG00000104894 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.04 | 0.10 | 0.03 | 0.02 | 0.09 | 0.05 | 0.06 | 0.03 | 0.01 | 0.02 | 0.02 | 0.03 | 0.03 | 0.05 | 0.04 | 0.04 | 0.00 | 0.07 | 0.18 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.05 | 0.04 | 0.32 | 0.05 | 0.06 | 0.05 | 0.05 | 0.14 | 0.18 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.05 | 0.00 | 0.13 | 0.02 | 0.12 | 0.00 | 0.00 | 0.02 | 0.02 |
| TXNDC11 | ENSG00000153066 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.21 | 0.04 | 0.00 | 0.00 | 0.04 | 0.00 | 0.07 | 0.02 | 0.07 | 0.03 | 0.04 | 0.01 | 0.07 | 0.02 | 0.06 | 0.03 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.01 | 0.20 | 0.07 | 0.23 | 0.02 | 0.09 | 0.01 | 0.14 | 0.02 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 |
| PSIP1 | ENSG00000164985 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.15 | 0.01 | 0.01 | 0.03 | 0.14 | 0.03 | 0.10 | 0.11 | 0.10 | 0.17 | 0.05 | 0.10 | 0.10 | 0.05 | 0.10 | 0.01 | 0.02 | 0.02 | 0.04 | 0.04 | 0.08 | 0.01 | 0.04 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.06 | 0.16 | 0.14 | 0.13 | 0.03 | 0.05 | 0.03 | 0.05 | 0.05 | 0.10 | 0.12 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.04 | 0.23 | 0.00 | 0.00 | 0.04 | 0.10 |
| CYP27A1 | ENSG00000135929 | 0.01 | 0.06 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.01 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 0.11 | 0.06 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.15 | 0.04 | 0.34 | 0.06 | 0.04 | 0.19 | 0.05 | 0.08 | 0.19 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 |
| PDE1A | ENSG00000115252 | 0.03 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.06 | 0.06 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.15 | 0.03 | 0.15 | 0.02 | 0.12 | 0.03 | 0.06 | 0.05 | 0.01 | 0.01 | 0.02 | 0.03 | 0.03 | 0.01 | 0.04 | 0.04 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 | 0.40 | 0.05 | 0.12 | 0.02 | 0.07 | 0.01 | 0.07 | 0.00 | 0.03 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| PLCH2 | ENSG00000149527 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.09 | 0.06 | 0.08 | 0.11 | 0.06 | 0.09 | 0.13 | 0.08 | 0.09 | 0.09 | 0.02 | 0.11 | 0.00 | 0.17 | 0.05 | 0.05 | 0.02 | 0.31 | 0.00 | 1.01 | 0.05 | 0.17 | 0.01 | 0.12 | 0.00 | 0.00 | 0.04 | 0.19 | 0.23 | 0.38 | 0.06 | 0.11 | 0.05 | 0.12 | 0.08 | 0.27 | 0.18 | 0.28 | 0.10 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.00 | 0.03 | 0.03 | 0.15 | 0.00 | 0.14 | 0.07 | 0.13 |
| AGER | ENSG00000204305 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.05 | 0.05 | 0.03 | 0.04 | 0.15 | 0.05 | 0.09 | 0.04 | 0.03 | 0.02 | 0.06 | 0.02 | 0.04 | 0.01 | 0.08 | 0.01 | 0.05 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.28 | 0.06 | 0.09 | 0.01 | 0.05 | 0.01 | 0.05 | 0.03 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.01 | 0.01 | 0.11 | 0.00 | 0.11 | 0.01 |
| TMX3 | ENSG00000166479 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.11 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.09 | 0.05 | 0.08 | 0.01 | 0.16 | 0.03 | 0.18 | 0.03 | 0.16 | 0.00 | 0.15 | 0.01 | 0.12 | 0.00 | 0.11 | 0.03 | 0.06 | 0.00 | 0.10 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.07 | 0.07 | 0.37 | 0.01 | 0.04 | 0.01 | 0.08 | 0.03 | 0.16 | 0.10 | 0.09 | 0.00 | 0.10 | 0.00 | 0.01 | 0.10 | 0.00 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.04 | 0.03 | 0.02 |
| ARNT | ENSG00000143437 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.65 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.46 | 0.01 | 0.31 | 0.00 | 0.08 | 0.01 | 0.24 | 0.00 | 0.24 | 0.00 | 0.03 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.40 | 0.01 | 0.43 | 0.01 | 0.23 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.42 | 0.00 | 0.76 | 0.02 | 0.21 | 0.00 | 0.34 | 0.00 | 0.61 | 0.00 | 0.47 | 0.02 | 0.13 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 |
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