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 |
| GAPDH | ENSG00000111640 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.06 | 0.07 | 0.17 | 0.01 | 0.11 | 0.01 | 0.08 | 0.05 | 0.06 | 0.05 | 0.06 | 0.02 | 0.05 | 0.02 | 0.05 | 0.05 | 0.04 | 0.04 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.37 | 0.08 | 0.05 | 0.02 | 0.10 | 0.02 | 0.12 | 0.03 | 0.11 | 0.13 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.05 | 0.04 |
| SCG2 | ENSG00000171951 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.05 | 0.01 | 0.03 | 0.01 | 0.29 | 0.00 | 0.02 | 0.00 | 0.10 | 0.03 | 0.04 | 0.03 | 0.19 | 0.01 | 0.19 | 0.04 | 0.14 | 0.05 | 0.05 | 0.02 | 0.02 | 0.01 | 0.02 | 0.07 | 0.03 | 0.03 | 0.05 | 0.00 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.16 | 0.19 | 0.01 | 0.36 | 0.03 | 0.05 | 0.13 | 0.05 | 0.06 | 0.21 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.06 |
| CDK2 | ENSG00000123374 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.07 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.08 | 0.03 | 0.17 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.08 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.26 | 0.04 | 0.03 | 0.00 | 0.15 | 0.00 | 0.21 | 0.07 | 0.21 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.02 | 0.03 | 0.03 | 0.05 | 0.00 | 0.00 | 0.05 | 0.03 |
| SF3B3 | ENSG00000189091 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.14 | 0.16 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.04 | 0.04 | 0.02 | 0.03 | 0.02 | 0.10 | 0.01 | 0.05 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.09 | 0.01 | 0.14 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.06 | 0.31 | 0.04 | 0.04 | 0.06 | 0.07 | 0.15 | 0.16 | 0.06 | 0.03 | 0.12 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.05 | 0.02 |
| CDC25C | ENSG00000158402 | 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 | 0.12 | 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 |
| PRPF4B | ENSG00000112739 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.20 | 0.09 | 0.00 | 0.05 | 0.02 | 0.01 | 0.10 | 0.02 | 0.10 | 0.08 | 0.05 | 0.06 | 0.08 | 0.23 | 0.05 | 0.11 | 0.03 | 0.03 | 0.02 | 0.06 | 0.00 | 0.07 | 0.16 | 0.02 | 0.06 | 0.03 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.12 | 0.08 | 0.44 | 0.10 | 0.10 | 0.06 | 0.10 | 0.02 | 0.21 | 0.05 | 0.08 | 0.14 | 0.04 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.02 | 0.03 | 0.03 | 0.03 | 0.22 | 0.00 | 0.23 | 0.00 |
| MBOAT2 | ENSG00000143797 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.02 | 0.17 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.05 | 0.02 | 0.09 | 0.05 | 0.03 | 0.04 | 0.07 | 0.07 | 0.04 | 0.04 | 0.01 | 0.01 | 0.03 | 0.04 | 0.01 | 0.03 | 0.12 | 0.01 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.05 | 0.27 | 0.15 | 0.08 | 0.01 | 0.12 | 0.04 | 0.28 | 0.07 | 0.04 | 0.12 | 0.16 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.03 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.03 | 0.04 |
| SLC45A3 | ENSG00000158715 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.06 | 0.05 | 0.01 | 0.00 | 0.12 | 0.00 | 0.14 | 0.01 | 0.09 | 0.01 | 0.05 | 0.00 | 0.18 | 0.07 | 0.06 | 0.02 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.28 | 0.08 | 0.07 | 0.00 | 0.14 | 0.01 | 0.33 | 0.00 | 0.05 | 0.17 | 0.05 | 0.02 | 0.01 | 0.00 | 0.21 | 0.04 | 0.00 | 0.01 | 0.05 | 0.02 | 0.09 | 0.00 | 0.18 | 0.02 |
| BCL2L1 | ENSG00000171552 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.34 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.14 | 0.01 | 0.29 | 0.00 | 0.20 | 0.00 | 0.08 | 0.00 | 0.08 | 0.00 | 0.18 | 0.00 | 0.22 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.35 | 0.02 | 0.32 | 0.00 | 0.22 | 0.00 | 1.30 | 0.00 | 0.14 | 0.02 | 0.24 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 |
| TMPRSS2 | ENSG00000184012 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.41 | 0.04 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.08 | 0.02 | 0.06 | 0.03 | 0.08 | 0.04 | 0.07 | 0.02 | 0.01 | 0.01 | 0.06 | 0.01 | 0.01 | 0.02 | 0.02 | 0.07 | 0.03 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.12 | 0.17 | 0.07 | 0.03 | 0.04 | 0.01 | 0.04 | 0.03 | 0.09 | 0.07 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 |
| COL1A2 | ENSG00000164692 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.07 | 0.01 | 0.23 | 0.01 | 0.25 | 0.00 | 0.67 | 0.02 | 0.31 | 0.01 | 0.04 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.13 | 0.02 | 0.18 | 0.01 | 0.10 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 | 0.16 | 0.06 | 0.05 | 0.01 | 0.04 | 0.01 | 0.08 | 0.03 | 0.07 | 0.04 | 0.12 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 |
| HNF4A | ENSG00000101076 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.22 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.07 | 0.01 | 0.02 | 0.02 | 0.13 | 0.00 | 0.22 | 0.00 | 0.22 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.18 | 0.05 | 0.03 | 0.03 | 0.08 | 0.01 | 0.43 | 0.00 | 0.12 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| MMP13 | ENSG00000137745 | 0.01 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.26 | 0.07 | 0.00 | 0.01 | 0.06 | 0.08 | 0.09 | 0.05 | 0.11 | 0.07 | 0.33 | 0.10 | 0.18 | 0.07 | 0.06 | 0.05 | 0.02 | 0.01 | 0.02 | 0.04 | 0.06 | 0.01 | 0.05 | 0.05 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.05 | 0.19 | 0.33 | 0.14 | 0.71 | 0.11 | 0.05 | 0.05 | 0.07 | 0.30 | 0.20 | 0.14 | 0.01 | 0.08 | 0.02 | 0.00 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.14 | 0.13 |
| MMP11 | ENSG00000099953 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.18 | 0.04 | 0.02 | 0.01 | 0.01 | 0.05 | 0.07 | 0.02 | 0.18 | 0.02 | 0.05 | 0.00 | 0.06 | 0.01 | 0.05 | 0.02 | 0.01 | 0.02 | 0.07 | 0.01 | 0.00 | 0.02 | 0.02 | 0.04 | 0.03 | 0.05 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.03 | 0.16 | 0.04 | 0.02 | 0.00 | 0.08 | 0.03 | 0.37 | 0.03 | 0.11 | 0.04 | 0.22 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.09 | 0.03 |
| REV3L | ENSG00000009413 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.29 | 0.02 | 0.13 | 0.00 | 0.01 | 0.02 | 0.14 | 0.01 | 0.05 | 0.04 | 0.05 | 0.02 | 0.03 | 0.04 | 0.09 | 0.05 | 0.07 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.15 | 0.05 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.13 | 0.09 | 0.07 | 0.25 | 0.01 | 0.03 | 0.08 | 0.02 | 0.14 | 0.03 | 0.19 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.21 | 0.00 | 0.02 | 0.02 | 0.06 | 0.05 | 0.03 | 0.00 | 0.14 |
| MDM2 | ENSG00000135679 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.60 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.36 | 0.01 | 0.24 | 0.01 | 0.26 | 0.02 | 0.42 | 0.01 | 0.43 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 | 0.11 | 0.01 | 0.09 | 0.00 | 0.26 | 0.01 | 0.33 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.29 | 0.02 | 0.27 | 0.04 | 0.09 | 0.01 | 0.05 | 0.01 | 0.46 | 0.07 | 1.93 | 0.04 | 0.26 | 0.00 | 0.00 | 0.01 | 0.12 | 0.00 | 0.06 | 0.02 | 0.74 | 0.03 | 0.00 | 0.00 | 0.32 | 0.01 |
| PSMA6 | ENSG00000100902 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.64 | 0.01 | 0.14 | 0.05 | 0.08 | 0.03 | 0.19 | 0.03 | 0.08 | 0.02 | 0.03 | 0.01 | 0.02 | 0.03 | 0.01 | 0.01 | 0.06 | 0.04 | 0.05 | 0.02 | 0.24 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.16 | 0.02 | 0.18 | 0.11 | 0.07 | 0.01 | 0.07 | 0.02 | 0.22 | 0.03 | 0.21 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.00 | 0.02 | 0.02 |
| MYT1 | ENSG00000196132 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.32 | 0.01 | 0.08 | 0.04 | 0.03 | 0.01 | 0.17 | 0.01 | 0.16 | 0.00 | 0.09 | 0.00 | 0.13 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.36 | 0.02 | 0.52 | 0.04 | 0.04 | 0.02 | 0.15 | 0.01 | 0.44 | 0.00 | 0.20 | 0.11 | 0.03 | 0.03 | 0.03 | 0.00 | 0.04 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.15 | 0.00 |
| SMARCA2 | ENSG00000080503 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 | 0.06 | 0.13 | 0.08 | 0.01 | 0.01 | 0.04 | 0.06 | 0.04 | 0.12 | 0.13 | 0.11 | 0.17 | 0.08 | 0.07 | 0.17 | 0.12 | 0.12 | 0.02 | 0.02 | 0.04 | 0.05 | 0.01 | 0.07 | 0.06 | 0.04 | 0.03 | 0.01 | 0.09 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.11 | 0.06 | 0.21 | 0.19 | 0.14 | 0.05 | 0.08 | 0.03 | 0.00 | 0.19 | 0.16 | 0.16 | 0.01 | 0.10 | 0.00 | 0.00 | 0.08 | 0.02 | 0.01 | 0.09 | 0.01 | 0.17 | 0.00 | 0.00 | 0.05 | 0.10 |
| LCK | ENSG00000182866 | 0.00 | 0.04 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.07 | 0.00 | 0.01 | 0.11 | 0.07 | 0.05 | 0.04 | 0.04 | 0.06 | 0.04 | 0.05 | 0.05 | 0.07 | 0.05 | 0.07 | 0.02 | 0.09 | 0.01 | 0.11 | 0.01 | 0.03 | 0.01 | 0.17 | 0.00 | 0.61 | 0.00 | 0.03 | 0.02 | 0.07 | 0.00 | 0.00 | 0.05 | 0.09 | 0.30 | 0.23 | 0.06 | 0.02 | 0.08 | 0.07 | 0.06 | 0.05 | 0.14 | 0.05 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.07 | 0.05 | 0.05 |
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