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 |
| LRRK1 | ENSG00000154237 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.03 | 0.07 | 0.03 | 0.03 | 0.02 | 0.06 | 0.00 | 0.08 | 0.02 | 0.26 | 0.02 | 0.11 | 0.02 | 0.26 | 0.02 | 0.25 | 0.02 | 0.05 | 0.01 | 0.08 | 0.02 | 0.07 | 0.00 | 0.13 | 0.07 | 0.05 | 0.01 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.21 | 0.04 | 0.45 | 0.07 | 0.18 | 0.02 | 0.08 | 0.02 | 0.14 | 0.04 | 0.28 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.20 | 0.02 |
| MLYCD | ENSG00000103150 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.08 | 0.00 | 0.26 | 0.09 | 0.04 | 0.00 | 0.00 | 0.01 | 0.17 | 0.01 | 0.09 | 0.04 | 0.07 | 0.04 | 0.04 | 0.05 | 0.06 | 0.03 | 0.04 | 0.01 | 0.03 | 0.02 | 0.03 | 0.01 | 0.04 | 0.00 | 0.06 | 0.05 | 0.01 | 0.06 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.08 | 0.05 | 0.32 | 0.03 | 0.04 | 0.00 | 0.08 | 0.01 | 0.24 | 0.05 | 0.08 | 0.00 | 0.10 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.00 | 0.02 | 0.01 | 0.09 |
| KCNQ2 | ENSG00000075043 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.31 | 0.01 | 0.07 | 0.04 | 0.03 | 0.02 | 0.16 | 0.01 | 0.16 | 0.00 | 0.09 | 0.00 | 0.11 | 0.01 | 0.02 | 0.00 | 0.12 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.33 | 0.02 | 0.50 | 0.04 | 0.04 | 0.03 | 0.13 | 0.01 | 0.44 | 0.00 | 0.19 | 0.09 | 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 |
| ST3GAL2 | ENSG00000157350 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.13 | 0.16 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.03 | 0.04 | 0.02 | 0.03 | 0.02 | 0.12 | 0.01 | 0.06 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.09 | 0.01 | 0.16 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.06 | 0.31 | 0.04 | 0.04 | 0.04 | 0.07 | 0.10 | 0.12 | 0.06 | 0.03 | 0.12 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.05 | 0.02 |
| ITGB7 | ENSG00000139626 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.04 | 0.02 | 0.02 | 0.03 | 0.04 | 0.05 | 0.05 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.01 | 0.01 | 0.09 | 0.01 | 0.21 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.12 | 0.05 | 0.03 | 0.00 | 0.09 | 0.01 | 0.38 | 0.05 | 0.02 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 |
| KLHL4 | ENSG00000102271 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.07 | 0.02 | 0.02 | 0.00 | 0.05 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.10 | 0.04 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.02 | 0.12 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 |
| ALPL | ENSG00000162551 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.09 | 0.00 | 0.01 | 0.04 | 0.23 | 0.05 | 0.06 | 0.03 | 0.12 | 0.03 | 0.07 | 0.03 | 0.10 | 0.05 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.08 | 0.02 | 0.22 | 0.00 | 1.06 | 0.10 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.19 | 0.10 | 0.45 | 0.04 | 0.09 | 0.06 | 0.13 | 0.12 | 0.21 | 0.17 | 0.10 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.02 | 0.04 | 0.10 | 0.00 | 0.12 | 0.07 | 0.09 |
| MFSD2A | ENSG00000168389 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.35 | 0.02 | 0.00 | 0.00 | 0.11 | 0.03 | 0.13 | 0.02 | 0.16 | 0.02 | 0.09 | 0.02 | 0.35 | 0.02 | 0.08 | 0.03 | 0.05 | 0.02 | 0.01 | 0.03 | 0.04 | 0.01 | 0.05 | 0.10 | 0.00 | 0.31 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.09 | 0.04 | 0.74 | 0.05 | 0.07 | 0.01 | 0.13 | 0.01 | 0.17 | 0.05 | 0.11 | 0.03 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.10 | 0.05 | 0.03 |
| PLCG2 | ENSG00000197943 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.08 | 0.01 | 0.25 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.02 | 0.08 | 0.05 | 0.06 | 0.03 | 0.04 | 0.06 | 0.04 | 0.04 | 0.05 | 0.02 | 0.02 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.05 | 0.05 | 0.01 | 0.05 | 0.06 | 0.01 | 0.01 | 0.00 | 0.01 | 0.04 | 0.07 | 0.06 | 0.33 | 0.02 | 0.03 | 0.02 | 0.08 | 0.01 | 0.24 | 0.05 | 0.06 | 0.00 | 0.10 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.00 | 0.02 | 0.03 | 0.08 |
| SGK2 | ENSG00000101049 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.06 | 0.01 | 0.01 | 0.02 | 0.09 | 0.00 | 0.17 | 0.00 | 0.18 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.13 | 0.06 | 0.03 | 0.04 | 0.06 | 0.01 | 0.19 | 0.00 | 0.15 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 |
| RAPGEF4 | ENSG00000091428 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.15 | 0.01 | 0.17 | 0.01 | 0.24 | 0.03 | 0.06 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.06 | 0.01 | 0.09 | 0.05 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.38 | 0.03 | 0.11 | 0.01 | 0.08 | 0.01 | 0.11 | 0.00 | 0.04 | 0.11 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| SPINT1 | ENSG00000166145 | 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 | 0.05 | 0.02 | 0.09 | 0.01 | 0.09 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.03 | 0.00 | 0.07 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.12 | 0.06 | 0.35 | 0.01 | 0.11 | 0.03 | 0.09 | 0.05 | 0.37 | 0.04 | 0.09 | 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 |
| UGT8 | ENSG00000174607 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.02 | 0.05 | 0.01 | 0.02 | 0.05 | 0.05 | 0.02 | 0.05 | 0.01 | 0.04 | 0.00 | 0.02 | 0.00 | 0.02 | 0.03 | 0.09 | 0.00 | 0.11 | 0.21 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.06 | 0.06 | 0.27 | 0.01 | 0.03 | 0.01 | 0.05 | 0.01 | 0.09 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 |
| RABGGTA | ENSG00000100949 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.15 | 0.03 | 0.10 | 0.07 | 0.05 | 0.07 | 0.11 | 0.05 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.06 | 0.00 | 0.03 | 0.08 | 0.01 | 0.00 | 0.02 | 0.28 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.03 | 0.17 | 0.13 | 0.03 | 0.03 | 0.05 | 0.03 | 0.27 | 0.12 | 0.22 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| SEMA7A | ENSG00000138623 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.02 | 0.06 | 0.02 | 0.02 | 0.03 | 0.08 | 0.03 | 0.05 | 0.03 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.17 | 0.15 | 0.12 | 0.01 | 0.04 | 0.04 | 0.18 | 0.03 | 0.06 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.12 | 0.01 |
| SLC4A4 | ENSG00000080493 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.16 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.09 | 0.03 | 0.23 | 0.01 | 0.08 | 0.01 | 0.11 | 0.03 | 0.06 | 0.03 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.03 | 0.06 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.10 | 0.02 | 0.29 | 0.10 | 0.05 | 0.03 | 0.04 | 0.02 | 0.12 | 0.05 | 0.08 | 0.05 | 0.11 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 |
| ADAMTS1 | ENSG00000154734 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.06 | 0.05 | 0.08 | 0.04 | 0.01 | 0.03 | 0.02 | 0.07 | 0.01 | 0.05 | 0.01 | 0.03 | 0.00 | 0.10 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.07 | 0.08 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.11 | 0.05 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.05 | 0.00 | 0.02 | 0.01 |
| CASP14 | ENSG00000105141 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.12 | 0.03 | 0.06 | 0.01 | 0.20 | 0.01 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.07 | 0.04 | 0.00 | 0.03 | 0.34 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.02 | 0.84 | 0.05 | 0.04 | 0.02 | 0.26 | 0.01 | 0.49 | 0.05 | 0.20 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.04 | 0.01 |
| CD96 | ENSG00000153283 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.14 | 0.03 | 0.05 | 0.01 | 0.10 | 0.02 | 0.06 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.10 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.06 | 0.02 | 0.34 | 0.04 | 0.04 | 0.01 | 0.04 | 0.01 | 0.09 | 0.08 | 0.12 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| PARP1 | ENSG00000143799 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.10 | 0.04 | 0.02 | 0.02 | 0.05 | 0.01 | 0.08 | 0.01 | 0.14 | 0.02 | 0.06 | 0.00 | 0.21 | 0.04 | 0.11 | 0.01 | 0.02 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.13 | 0.03 | 0.18 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.23 | 0.02 | 0.41 | 0.05 | 0.07 | 0.02 | 0.10 | 0.02 | 0.30 | 0.00 | 0.08 | 0.23 | 0.03 | 0.05 | 0.02 | 0.00 | 0.02 | 0.18 | 0.02 | 0.02 | 0.02 | 0.05 | 0.09 | 0.03 | 0.12 | 0.05 |
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