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 |
| CHIT1 | ENSG00000133063 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.06 | 0.02 | 0.00 | 0.10 | 0.00 | 0.13 | 0.00 | 0.11 | 0.01 | 0.05 | 0.01 | 0.17 | 0.06 | 0.06 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.20 | 0.01 | 0.18 | 0.02 | 0.08 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.26 | 0.00 | 0.32 | 0.07 | 0.06 | 0.00 | 0.10 | 0.01 | 0.17 | 0.00 | 0.10 | 0.13 | 0.05 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.06 | 0.01 | 0.16 | 0.00 | 0.09 | 0.00 | 0.18 | 0.01 |
| RXFP2 | ENSG00000133105 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.13 | 0.16 | 0.10 | 0.00 | 0.02 | 0.00 | 0.17 | 0.02 | 0.08 | 0.02 | 0.11 | 0.02 | 0.14 | 0.15 | 0.06 | 0.18 | 0.03 | 0.14 | 0.00 | 0.21 | 0.04 | 0.00 | 0.01 | 0.03 | 0.15 | 0.00 | 0.14 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.09 | 0.09 | 0.18 | 0.03 | 0.16 | 0.00 | 0.05 | 0.01 | 0.15 | 0.09 | 0.29 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.01 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.08 | 0.02 |
| MORC4 | ENSG00000133131 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.01 | 0.13 | 0.01 | 0.03 | 0.01 | 0.13 | 0.02 | 0.08 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.08 | 0.05 | 0.03 | 0.01 | 0.02 | 0.02 | 0.11 | 0.02 | 0.09 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 |
| CNDP2 | ENSG00000133313 | 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 | 0.09 | 0.04 | 0.11 | 0.03 | 0.17 | 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 | 0.10 | 0.00 | 0.01 | 0.08 | 0.05 | 0.01 | 0.02 | 0.01 | 0.07 | 0.00 | 0.04 | 0.02 | 0.03 |
| GSTT2B | ENSG00000133433 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.19 | 0.04 | 0.02 | 0.02 | 0.01 | 0.05 | 0.08 | 0.02 | 0.19 | 0.02 | 0.04 | 0.00 | 0.06 | 0.02 | 0.05 | 0.02 | 0.01 | 0.01 | 0.07 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.03 | 0.18 | 0.05 | 0.02 | 0.00 | 0.07 | 0.03 | 0.37 | 0.03 | 0.10 | 0.04 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.03 |
| SLC2A11 | ENSG00000133460 | 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 | 0.08 | 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 | 0.01 | 0.02 | 0.03 | 0.03 | 0.05 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.18 | 0.04 | 0.03 | 0.00 | 0.06 | 0.03 | 0.37 | 0.03 | 0.10 | 0.04 | 0.21 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 |
| GGT2 | ENSG00000133475 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.19 | 0.06 | 0.03 | 0.01 | 0.04 | 0.05 | 0.14 | 0.03 | 0.29 | 0.07 | 0.08 | 0.03 | 0.06 | 0.07 | 0.08 | 0.04 | 0.02 | 0.01 | 0.05 | 0.03 | 0.00 | 0.02 | 0.03 | 0.03 | 0.03 | 0.10 | 0.06 | 0.14 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.25 | 0.07 | 0.04 | 0.01 | 0.08 | 0.06 | 0.43 | 0.04 | 0.21 | 0.07 | 0.29 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.14 | 0.03 |
| NTS | ENSG00000133636 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.04 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.05 | 0.05 | 0.04 | 0.00 | 0.03 | 0.09 | 0.07 | 0.02 | 0.04 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.07 | 0.02 | 0.02 | 0.00 | 0.08 | 0.12 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.09 | 0.05 | 0.08 | 0.19 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.16 | 0.42 | 0.05 | 0.01 | 0.02 | 0.00 | 0.02 | 0.09 | 0.02 | 0.00 | 0.02 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.07 |
| LARS | ENSG00000133706 | 0.31 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.06 | 0.04 | 0.04 | 0.01 | 0.04 | 0.01 | 0.05 | 0.02 | 0.04 | 0.02 | 0.05 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.02 | 0.08 | 0.02 | 0.09 | 0.01 | 0.22 | 0.04 | 0.00 | 0.04 | 0.01 | 0.00 | 0.03 | 0.02 | 0.14 | 0.09 | 0.02 | 0.01 | 0.02 | 0.02 | 0.09 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.06 | 0.01 | 0.02 | 0.00 | 0.03 | 0.04 | 0.14 |
| SARAF | ENSG00000133872 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.12 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.05 | 0.02 | 0.05 | 0.03 | 0.02 | 0.08 | 0.06 | 0.04 | 0.04 | 0.04 | 0.05 | 0.01 | 0.09 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.08 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.02 | 0.26 | 0.00 | 0.02 | 0.02 | 0.06 | 0.12 | 0.10 | 0.05 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
| DPF2 | ENSG00000133884 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.07 | 0.03 | 0.07 | 0.02 | 0.19 | 0.02 | 0.15 | 0.04 | 0.04 | 0.03 | 0.01 | 0.02 | 0.04 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.09 | 0.19 | 0.04 | 0.10 | 0.01 | 0.09 | 0.03 | 0.22 | 0.06 | 0.09 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.06 |
| ADAM20 | ENSG00000134007 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.04 | 0.03 | 0.05 | 0.04 | 0.02 | 0.05 | 0.03 | 0.02 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.01 | 0.00 | 0.09 | 0.00 | 0.33 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.11 | 0.08 | 0.26 | 0.03 | 0.02 | 0.01 | 0.02 | 0.05 | 0.04 | 0.05 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.07 | 0.03 | 0.00 | 0.01 | 0.04 |
| CCNB1 | ENSG00000134057 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.22 | 0.01 | 0.15 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.08 | 0.01 | 0.09 | 0.01 | 0.07 | 0.01 | 0.16 | 0.01 | 0.14 | 0.01 | 0.07 | 0.00 | 0.09 | 0.00 | 0.07 | 0.00 | 0.04 | 0.00 | 0.13 | 0.07 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.01 | 0.72 | 0.00 | 0.07 | 0.01 | 0.11 | 0.00 | 0.35 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| CD180 | ENSG00000134061 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.19 | 0.02 | 0.16 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.01 | 0.10 | 0.02 | 0.07 | 0.01 | 0.16 | 0.01 | 0.12 | 0.00 | 0.07 | 0.00 | 0.09 | 0.00 | 0.07 | 0.00 | 0.03 | 0.00 | 0.13 | 0.08 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.10 | 0.02 | 0.67 | 0.01 | 0.07 | 0.00 | 0.12 | 0.00 | 0.35 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 |
| CAMK1 | ENSG00000134072 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.06 | 0.42 | 0.02 | 0.00 | 0.03 | 0.05 | 0.06 | 0.05 | 0.05 | 0.03 | 0.03 | 0.03 | 0.02 | 0.09 | 0.05 | 0.07 | 0.06 | 0.00 | 0.04 | 0.01 | 0.06 | 0.01 | 0.02 | 0.08 | 0.01 | 0.00 | 0.18 | 0.08 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.13 | 0.02 | 0.18 | 0.21 | 0.02 | 0.02 | 0.05 | 0.03 | 0.22 | 0.14 | 0.23 | 0.03 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
| CHL1 | ENSG00000134121 | 0.00 | 0.18 | 0.00 | 0.02 | 0.07 | 0.00 | 0.01 | 0.04 | 0.24 | 0.05 | 0.00 | 0.05 | 0.04 | 0.14 | 0.02 | 0.06 | 0.03 | 0.08 | 0.03 | 0.05 | 0.03 | 0.12 | 0.03 | 0.11 | 0.00 | 0.06 | 0.03 | 0.07 | 0.01 | 0.02 | 0.05 | 0.03 | 0.00 | 0.18 | 0.07 | 0.03 | 0.00 | 0.05 | 0.00 | 0.01 | 0.12 | 0.05 | 0.14 | 0.28 | 0.04 | 0.03 | 0.04 | 0.04 | 0.05 | 0.23 | 0.21 | 0.07 | 0.05 | 0.07 | 0.00 | 0.00 | 0.05 | 0.05 | 0.04 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.06 |
| GSTM1 | ENSG00000134184 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.33 | 0.01 | 0.13 | 0.01 | 0.14 | 0.00 | 0.12 | 0.06 | 0.12 | 0.02 | 0.07 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.04 | 0.10 | 0.17 | 0.14 | 0.01 | 0.08 | 0.05 | 0.03 | 0.08 | 0.06 | 0.05 | 0.10 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.07 | 0.10 |
| REG4 | ENSG00000134193 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.20 | 0.03 | 0.00 | 0.00 | 0.01 | 0.14 | 0.04 | 0.12 | 0.12 | 0.15 | 0.07 | 0.16 | 0.15 | 0.10 | 0.07 | 0.05 | 0.02 | 0.04 | 0.04 | 0.03 | 0.17 | 0.01 | 0.06 | 0.04 | 0.05 | 0.01 | 0.10 | 0.03 | 0.04 | 0.26 | 0.00 | 0.00 | 0.13 | 0.05 | 0.23 | 0.09 | 0.07 | 0.05 | 0.04 | 0.02 | 0.13 | 0.04 | 0.12 | 0.11 | 0.05 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.03 | 0.37 | 0.05 |
| TSHB | ENSG00000134200 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.30 | 0.02 | 0.14 | 0.02 | 0.17 | 0.00 | 0.16 | 0.09 | 0.17 | 0.03 | 0.08 | 0.00 | 0.07 | 0.05 | 0.07 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.15 | 0.02 | 0.05 | 0.03 | 0.26 | 0.00 | 0.00 | 0.04 | 0.08 | 0.16 | 0.13 | 0.01 | 0.08 | 0.02 | 0.03 | 0.14 | 0.06 | 0.04 | 0.12 | 0.03 | 0.03 | 0.00 | 0.00 | 0.03 | 0.09 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.13 | 0.10 |
| GSTM3 | ENSG00000134202 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.33 | 0.01 | 0.13 | 0.01 | 0.14 | 0.00 | 0.12 | 0.06 | 0.12 | 0.02 | 0.07 | 0.00 | 0.07 | 0.00 | 0.07 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.04 | 0.10 | 0.17 | 0.14 | 0.01 | 0.08 | 0.05 | 0.03 | 0.08 | 0.06 | 0.05 | 0.10 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.07 | 0.10 |
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