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 |
| BCAM | ENSG00000187244 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.14 | 0.02 | 0.00 | 0.00 | 0.05 | 0.05 | 0.14 | 0.04 | 0.13 | 0.08 | 0.07 | 0.02 | 0.09 | 0.05 | 0.18 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.09 | 0.02 | 0.08 | 0.03 | 0.12 | 0.03 | 0.24 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.05 | 0.20 | 0.29 | 0.21 | 0.02 | 0.13 | 0.04 | 0.31 | 0.17 | 0.08 | 0.16 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.02 | 0.12 | 0.02 | 0.09 | 0.00 | 0.00 | 0.02 | 0.02 |
| IL2RA | ENSG00000134460 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.40 | 0.00 | 0.00 | 0.00 | 0.02 | 0.14 | 0.04 | 0.05 | 0.04 | 0.07 | 0.02 | 0.04 | 0.09 | 0.06 | 0.07 | 0.05 | 0.02 | 0.02 | 0.02 | 0.00 | 0.03 | 0.03 | 0.02 | 0.02 | 0.00 | 0.05 | 0.05 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.19 | 0.01 | 0.36 | 0.10 | 0.03 | 0.01 | 0.05 | 0.01 | 0.17 | 0.00 | 0.07 | 0.12 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.00 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.02 |
| LBP | ENSG00000129988 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.03 | 0.10 | 0.02 | 0.02 | 0.01 | 0.06 | 0.01 | 0.08 | 0.00 | 0.08 | 0.00 | 0.17 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.10 | 0.07 | 0.05 | 0.02 | 0.04 | 0.01 | 0.18 | 0.00 | 0.12 | 0.05 | 0.00 | 0.01 | 0.00 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 |
| HSD17B12 | ENSG00000149084 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.08 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.09 | 0.04 | 0.09 | 0.02 | 0.16 | 0.04 | 0.07 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.06 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.03 | 0.12 | 0.07 | 0.08 | 0.02 | 0.04 | 0.02 | 0.07 | 0.04 | 0.12 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.02 | 0.05 |
| SIK2 | ENSG00000170145 | 0.00 | 0.01 | 0.00 | 0.07 | 0.02 | 0.02 | 0.01 | 0.08 | 0.04 | 0.11 | 0.00 | 0.00 | 0.02 | 0.12 | 0.05 | 0.09 | 0.05 | 0.10 | 0.04 | 0.17 | 0.05 | 0.14 | 0.05 | 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 | 0.05 | 0.00 | 0.00 | 0.03 | 0.23 | 0.16 | 0.17 | 0.05 | 0.28 | 0.02 | 0.07 | 0.09 | 0.19 | 0.03 | 0.25 | 0.00 | 0.17 | 0.02 | 0.00 | 0.10 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.27 |
| THSD4 | ENSG00000187720 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.03 | 0.00 | 0.00 | 0.09 | 0.02 | 0.04 | 0.02 | 0.07 | 0.02 | 0.04 | 0.03 | 0.06 | 0.05 | 0.07 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.30 | 0.13 | 0.11 | 0.02 | 0.05 | 0.08 | 0.27 | 0.22 | 0.09 | 0.08 | 0.01 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.11 | 0.00 |
| SCN9A | ENSG00000169432 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.10 | 0.03 | 0.08 | 0.01 | 0.11 | 0.03 | 0.02 | 0.04 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.01 | 0.05 | 0.05 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.31 | 0.05 | 0.06 | 0.01 | 0.05 | 0.02 | 0.03 | 0.00 | 0.05 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| COL4A2 | ENSG00000134871 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.02 | 0.23 | 0.02 | 0.00 | 0.01 | 0.03 | 0.00 | 0.12 | 0.04 | 0.17 | 0.06 | 0.14 | 0.02 | 0.16 | 0.04 | 0.16 | 0.04 | 0.13 | 0.01 | 0.17 | 0.01 | 0.02 | 0.02 | 0.30 | 0.01 | 0.06 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.04 | 0.26 | 0.09 | 0.23 | 0.02 | 0.11 | 0.02 | 0.47 | 0.06 | 0.28 | 0.15 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.12 | 0.06 | 0.02 | 0.05 | 0.03 | 0.05 | 0.00 | 0.06 | 0.07 |
| SLC15A4 | ENSG00000139370 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.02 | 0.02 | 0.08 | 0.08 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 | 0.05 | 0.06 | 0.04 | 0.06 | 0.02 | 0.04 | 0.09 | 0.07 | 0.06 | 0.04 | 0.02 | 0.01 | 0.05 | 0.02 | 0.00 | 0.07 | 0.03 | 0.11 | 0.03 | 0.17 | 0.05 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.04 | 0.09 | 0.13 | 0.27 | 0.04 | 0.01 | 0.02 | 0.06 | 0.04 | 0.16 | 0.15 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.00 | 0.03 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.09 |
| AOAH | ENSG00000136250 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.06 | 0.03 | 0.03 | 0.01 | 0.14 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.13 | 0.09 | 0.01 | 0.00 | 0.05 | 0.01 | 0.05 | 0.00 | 0.09 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 |
| KLK7 | ENSG00000169035 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.08 | 0.07 | 0.10 | 0.03 | 0.02 | 0.07 | 0.03 | 0.09 | 0.03 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.04 | 0.05 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.04 | 0.10 | 0.30 | 0.06 | 0.07 | 0.04 | 0.05 | 0.24 | 0.13 | 0.03 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.01 | 0.14 | 0.00 | 0.00 | 0.03 | 0.03 |
| PAMR1 | ENSG00000149090 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.12 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 | 0.07 | 0.01 | 0.15 | 0.02 | 0.15 | 0.01 | 0.25 | 0.02 | 0.26 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.02 | 0.05 | 0.00 | 0.00 | 0.15 | 0.01 | 0.17 | 0.06 | 0.15 | 0.01 | 0.07 | 0.02 | 0.04 | 0.02 | 0.15 | 0.09 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.05 | 0.02 |
| TNC | ENSG00000041982 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.06 | 0.01 | 0.05 | 0.01 | 0.13 | 0.01 | 0.07 | 0.02 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.03 | 0.04 | 0.06 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.09 | 0.11 | 0.04 | 0.00 | 0.01 | 0.04 | 0.00 | 0.15 | 0.09 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| DUSP26 | ENSG00000133878 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.08 | 0.06 | 0.00 | 0.00 | 0.05 | 0.06 | 0.01 | 0.04 | 0.14 | 0.06 | 0.09 | 0.02 | 0.16 | 0.08 | 0.02 | 0.03 | 0.04 | 0.05 | 0.04 | 0.08 | 0.00 | 0.02 | 0.03 | 0.08 | 0.00 | 0.09 | 0.08 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.14 | 0.09 | 0.06 | 0.19 | 0.01 | 0.02 | 0.02 | 0.07 | 0.26 | 0.19 | 0.04 | 0.10 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 |
| CAPZA2 | ENSG00000198898 | 0.03 | 0.01 | 0.15 | 0.00 | 0.07 | 0.00 | 0.02 | 0.04 | 0.09 | 0.02 | 0.00 | 0.01 | 0.05 | 0.03 | 0.18 | 0.03 | 0.13 | 0.05 | 0.06 | 0.07 | 0.18 | 0.16 | 0.18 | 0.05 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.03 | 0.17 | 0.03 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.28 | 0.07 | 0.04 | 0.05 | 0.04 | 0.03 | 0.08 | 0.08 | 0.12 | 0.03 | 0.03 | 0.02 | 0.00 | 0.03 | 0.09 | 0.04 | 0.12 | 0.00 | 0.16 | 0.00 | 0.00 | 0.00 | 0.13 | 0.02 |
| IRAK1 | ENSG00000184216 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.22 | 0.01 | 0.19 | 0.02 | 0.14 | 0.00 | 0.23 | 0.01 | 0.16 | 0.02 | 0.05 | 0.00 | 0.10 | 0.01 | 0.06 | 0.00 | 0.14 | 0.03 | 0.10 | 0.01 | 0.12 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.03 | 0.47 | 0.09 | 0.23 | 0.02 | 0.13 | 0.03 | 0.09 | 0.07 | 0.24 | 0.07 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.03 | 0.01 | 0.05 | 0.00 | 0.06 | 0.01 |
| CSPG4 | ENSG00000173546 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.04 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.02 | 0.09 | 0.01 | 0.02 | 0.02 | 0.08 | 0.03 | 0.07 | 0.04 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.01 | 0.05 | 0.03 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.03 | 0.18 | 0.14 | 0.12 | 0.01 | 0.04 | 0.05 | 0.14 | 0.05 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.01 |
| LINGO2 | ENSG00000174482 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.07 | 0.11 | 0.00 | 0.00 | 0.01 | 0.55 | 0.05 | 0.08 | 0.18 | 0.23 | 0.05 | 0.10 | 0.19 | 0.10 | 0.04 | 0.11 | 0.01 | 0.00 | 0.00 | 0.02 | 0.12 | 0.11 | 0.02 | 0.03 | 0.00 | 0.01 | 0.10 | 0.10 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.11 | 0.15 | 0.02 | 0.04 | 0.04 | 0.04 | 0.06 | 0.14 | 0.10 | 0.14 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.09 | 0.02 | 0.37 | 0.00 | 0.00 | 0.03 | 0.14 |
| ERBB4 | ENSG00000178568 | 0.02 | 0.05 | 0.04 | 0.03 | 0.00 | 0.09 | 0.03 | 0.03 | 0.03 | 0.30 | 0.00 | 0.00 | 0.00 | 0.13 | 0.03 | 0.03 | 0.05 | 0.19 | 0.02 | 0.17 | 0.05 | 0.16 | 0.05 | 0.06 | 0.02 | 0.01 | 0.02 | 0.02 | 0.07 | 0.03 | 0.04 | 0.05 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.05 | 0.05 | 0.23 | 0.17 | 0.03 | 0.32 | 0.05 | 0.08 | 0.06 | 0.19 | 0.08 | 0.17 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.03 | 0.01 | 0.01 | 0.02 | 0.04 | 0.03 | 0.05 |
| CBR3 | ENSG00000159231 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.05 | 0.02 | 0.03 | 0.03 | 0.04 | 0.04 | 0.05 | 0.02 | 0.02 | 0.03 | 0.05 | 0.01 | 0.01 | 0.01 | 0.01 | 0.05 | 0.03 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.11 | 0.08 | 0.10 | 0.01 | 0.02 | 0.01 | 0.04 | 0.03 | 0.04 | 0.07 | 0.03 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
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