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 |
| MMP3 | ENSG00000149968 | 0.01 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.25 | 0.07 | 0.00 | 0.01 | 0.06 | 0.06 | 0.11 | 0.05 | 0.10 | 0.07 | 0.37 | 0.10 | 0.20 | 0.07 | 0.07 | 0.05 | 0.02 | 0.01 | 0.02 | 0.04 | 0.05 | 0.01 | 0.05 | 0.06 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.06 | 0.19 | 0.36 | 0.13 | 0.78 | 0.11 | 0.05 | 0.05 | 0.10 | 0.26 | 0.23 | 0.15 | 0.01 | 0.08 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.12 | 0.13 |
| OR8K1 | ENSG00000150261 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.14 | 0.03 | 0.00 | 0.00 | 0.06 | 0.03 | 0.03 | 0.03 | 0.09 | 0.03 | 0.12 | 0.01 | 0.16 | 0.03 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.03 | 0.02 | 0.05 | 0.07 | 0.05 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.07 | 0.11 | 0.04 | 0.05 | 0.01 | 0.04 | 0.02 | 0.28 | 0.02 | 0.07 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 |
| OR5M9 | ENSG00000150269 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.14 | 0.03 | 0.00 | 0.00 | 0.06 | 0.03 | 0.03 | 0.03 | 0.09 | 0.03 | 0.12 | 0.01 | 0.16 | 0.03 | 0.01 | 0.05 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.02 | 0.05 | 0.07 | 0.05 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.07 | 0.12 | 0.04 | 0.06 | 0.02 | 0.04 | 0.02 | 0.28 | 0.08 | 0.09 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 |
| CTF1 | ENSG00000150281 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.01 | 0.11 | 0.02 | 0.03 | 0.01 | 0.10 | 0.00 | 0.07 | 0.00 | 0.07 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.09 | 0.03 | 0.02 | 0.03 | 0.15 | 0.00 | 0.75 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| FCGR1A | ENSG00000150337 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.50 | 0.04 | 0.02 | 0.00 | 0.10 | 0.13 | 0.38 | 0.12 | 0.28 | 0.13 | 0.10 | 0.16 | 0.23 | 0.11 | 0.19 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.05 | 0.01 | 0.33 | 0.03 | 0.39 | 0.01 | 0.17 | 0.03 | 0.10 | 0.26 | 0.00 | 0.00 | 0.36 | 0.05 | 0.60 | 0.09 | 0.15 | 0.06 | 0.25 | 0.02 | 0.41 | 0.04 | 0.41 | 0.12 | 0.12 | 0.03 | 0.00 | 0.00 | 0.28 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.03 | 0.17 | 0.05 |
| HNMT | ENSG00000150540 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.20 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.04 | 0.03 | 0.02 | 0.07 | 0.04 | 0.03 | 0.04 | 0.07 | 0.11 | 0.03 | 0.06 | 0.00 | 0.04 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.05 | 0.09 | 0.03 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.06 | 0.10 | 0.15 | 0.02 | 0.02 | 0.02 | 0.02 | 0.07 | 0.00 | 0.13 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| PDCD4 | ENSG00000150593 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.01 | 0.10 | 0.00 | 0.02 | 0.01 | 0.20 | 0.04 | 0.03 | 0.04 | 0.07 | 0.01 | 0.03 | 0.04 | 0.08 | 0.05 | 0.07 | 0.02 | 0.07 | 0.01 | 0.07 | 0.01 | 0.01 | 0.01 | 0.08 | 0.11 | 0.21 | 0.06 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.10 | 0.14 | 0.24 | 0.01 | 0.07 | 0.04 | 0.07 | 0.03 | 0.07 | 0.04 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.09 | 0.01 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 |
| ADRA2A | ENSG00000150594 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.10 | 0.00 | 0.02 | 0.01 | 0.22 | 0.04 | 0.03 | 0.04 | 0.07 | 0.01 | 0.03 | 0.03 | 0.08 | 0.05 | 0.06 | 0.01 | 0.07 | 0.01 | 0.07 | 0.01 | 0.01 | 0.01 | 0.09 | 0.11 | 0.21 | 0.06 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.10 | 0.14 | 0.24 | 0.01 | 0.07 | 0.03 | 0.07 | 0.03 | 0.07 | 0.06 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.09 | 0.01 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 |
| CNDP1 | ENSG00000150656 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.10 | 0.03 | 0.11 | 0.04 | 0.18 | 0.05 | 0.19 | 0.03 | 0.16 | 0.01 | 0.11 | 0.01 | 0.11 | 0.00 | 0.06 | 0.05 | 0.06 | 0.00 | 0.18 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.08 | 0.08 | 0.42 | 0.02 | 0.05 | 0.03 | 0.08 | 0.00 | 0.10 | 0.15 | 0.10 | 0.00 | 0.12 | 0.00 | 0.01 | 0.08 | 0.05 | 0.01 | 0.02 | 0.01 | 0.07 | 0.00 | 0.04 | 0.02 | 0.03 |
| IL18 | ENSG00000150782 | 0.00 | 0.01 | 0.00 | 0.07 | 0.02 | 0.02 | 0.01 | 0.08 | 0.02 | 0.11 | 0.00 | 0.00 | 0.06 | 0.16 | 0.03 | 0.10 | 0.05 | 0.10 | 0.04 | 0.16 | 0.04 | 0.13 | 0.04 | 0.08 | 0.01 | 0.02 | 0.01 | 0.05 | 0.02 | 0.01 | 0.01 | 0.08 | 0.01 | 0.20 | 0.00 | 0.07 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.23 | 0.16 | 0.18 | 0.04 | 0.27 | 0.01 | 0.06 | 0.09 | 0.19 | 0.02 | 0.24 | 0.00 | 0.17 | 0.02 | 0.00 | 0.10 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.27 |
| PRSS53 | ENSG00000151006 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.01 | 0.10 | 0.01 | 0.03 | 0.02 | 0.08 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.08 | 0.03 | 0.02 | 0.03 | 0.12 | 0.00 | 0.52 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SLC7A11 | ENSG00000151012 | 0.01 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.02 | 0.03 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.04 | 0.04 | 0.10 | 0.02 | 0.03 | 0.05 | 0.06 | 0.06 | 0.05 | 0.01 | 0.04 | 0.02 | 0.04 | 0.00 | 0.02 | 0.05 | 0.05 | 0.00 | 0.03 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.09 | 0.17 | 0.03 | 0.06 | 0.03 | 0.03 | 0.04 | 0.04 | 0.09 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 |
| LYZL2 | ENSG00000151033 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.01 | 0.02 | 0.02 | 0.06 | 0.02 | 0.06 | 0.01 | 0.03 | 0.02 | 0.07 | 0.01 | 0.08 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.17 | 0.04 | 0.00 | 0.01 | 0.03 | 0.01 | 0.11 | 0.00 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| KCNA6 | ENSG00000151079 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.07 | 0.17 | 0.02 | 0.15 | 0.01 | 0.10 | 0.03 | 0.05 | 0.05 | 0.12 | 0.02 | 0.11 | 0.02 | 0.09 | 0.05 | 0.03 | 0.04 | 0.14 | 0.05 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.04 | 0.34 | 0.08 | 0.05 | 0.02 | 0.07 | 0.02 | 0.21 | 0.02 | 0.20 | 0.12 | 0.57 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.00 | 0.06 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 |
| EIF4E | ENSG00000151247 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.02 | 0.11 | 0.02 | 0.04 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.09 | 0.00 | 0.03 | 0.04 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.27 | 0.01 | 0.02 | 0.02 | 0.04 | 0.12 | 0.11 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 |
| ATP6V1G3 | ENSG00000151418 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.12 | 0.05 | 0.02 | 0.00 | 0.10 | 0.00 | 0.11 | 0.01 | 0.08 | 0.03 | 0.05 | 0.01 | 0.13 | 0.06 | 0.05 | 0.01 | 0.03 | 0.00 | 0.11 | 0.03 | 0.01 | 0.00 | 0.22 | 0.01 | 0.20 | 0.02 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.20 | 0.01 | 0.28 | 0.05 | 0.07 | 0.00 | 0.07 | 0.01 | 0.07 | 0.03 | 0.09 | 0.11 | 0.07 | 0.00 | 0.01 | 0.01 | 0.26 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.17 | 0.02 |
| QDPR | ENSG00000151552 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.02 | 0.07 | 0.02 | 0.05 | 0.04 | 0.05 | 0.03 | 0.03 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.02 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.16 | 0.06 | 0.01 | 0.01 | 0.04 | 0.03 | 0.06 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.05 | 0.00 | 0.06 | 0.01 |
| AKR1C2 | ENSG00000151632 | 0.02 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.35 | 0.03 | 0.00 | 0.00 | 0.02 | 0.14 | 0.13 | 0.07 | 0.08 | 0.13 | 0.03 | 0.07 | 0.15 | 0.10 | 0.09 | 0.03 | 0.03 | 0.03 | 0.02 | 0.00 | 0.03 | 0.03 | 0.07 | 0.03 | 0.00 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.19 | 0.02 | 0.36 | 0.11 | 0.04 | 0.02 | 0.04 | 0.01 | 0.19 | 0.00 | 0.06 | 0.10 | 0.01 | 0.04 | 0.00 | 0.00 | 0.07 | 0.07 | 0.08 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.04 | 0.03 |
| ADAM8 | ENSG00000151651 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.10 | 0.00 | 0.02 | 0.02 | 0.14 | 0.04 | 0.06 | 0.06 | 0.06 | 0.03 | 0.04 | 0.05 | 0.10 | 0.08 | 0.08 | 0.02 | 0.06 | 0.02 | 0.06 | 0.01 | 0.01 | 0.02 | 0.10 | 0.14 | 0.17 | 0.09 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.12 | 0.25 | 0.23 | 0.03 | 0.06 | 0.06 | 0.06 | 0.08 | 0.04 | 0.06 | 0.18 | 0.03 | 0.17 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.14 | 0.00 | 0.17 | 0.00 | 0.00 | 0.01 | 0.11 |
| ITIH2 | ENSG00000151655 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.44 | 0.00 | 0.00 | 0.00 | 0.02 | 0.11 | 0.03 | 0.05 | 0.03 | 0.07 | 0.02 | 0.03 | 0.09 | 0.05 | 0.06 | 0.04 | 0.01 | 0.02 | 0.02 | 0.00 | 0.03 | 0.02 | 0.01 | 0.02 | 0.00 | 0.05 | 0.07 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 | 0.27 | 0.11 | 0.03 | 0.02 | 0.03 | 0.01 | 0.18 | 0.00 | 0.04 | 0.08 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 |
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