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 |
| RPS6KA5 | ENSG00000100784 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.04 | 0.09 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.07 | 0.05 | 0.11 | 0.03 | 0.04 | 0.05 | 0.08 | 0.08 | 0.04 | 0.06 | 0.00 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.31 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.09 | 0.20 | 0.18 | 0.07 | 0.09 | 0.04 | 0.03 | 0.06 | 0.05 | 0.05 | 0.12 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| ITPR2 | ENSG00000123104 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.13 | 0.04 | 0.00 | 0.00 | 0.02 | 0.01 | 0.26 | 0.03 | 0.20 | 0.01 | 0.05 | 0.01 | 0.42 | 0.04 | 0.32 | 0.01 | 0.03 | 0.01 | 0.16 | 0.04 | 0.08 | 0.02 | 0.03 | 0.04 | 0.05 | 0.05 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.13 | 0.03 | 0.52 | 0.05 | 0.05 | 0.01 | 0.11 | 0.01 | 0.34 | 0.01 | 0.21 | 0.12 | 0.60 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.07 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 |
| EGF | ENSG00000138798 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.03 | 0.03 | 0.05 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.09 | 0.00 | 0.11 | 0.12 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.04 | 0.26 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.11 | 0.09 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 |
| COL14A1 | ENSG00000187955 | 0.02 | 0.00 | 0.01 | 0.00 | 0.09 | 0.00 | 0.07 | 0.01 | 0.26 | 0.02 | 0.02 | 0.01 | 0.05 | 0.03 | 0.26 | 0.01 | 0.31 | 0.01 | 0.26 | 0.00 | 0.51 | 0.01 | 0.29 | 0.01 | 0.15 | 0.00 | 0.26 | 0.00 | 0.11 | 0.01 | 0.37 | 0.01 | 0.25 | 0.01 | 0.04 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.52 | 0.02 | 1.39 | 0.05 | 0.19 | 0.00 | 0.19 | 0.00 | 0.35 | 0.00 | 0.16 | 0.07 | 0.03 | 0.02 | 0.02 | 0.00 | 0.21 | 0.00 | 0.20 | 0.00 | 0.02 | 0.01 | 0.53 | 0.00 | 0.17 | 0.01 |
| GLI2 | ENSG00000074047 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.13 | 0.06 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.07 | 0.01 | 0.15 | 0.02 | 0.13 | 0.01 | 0.32 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.04 | 0.00 | 0.01 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.12 | 0.14 | 0.03 | 0.02 | 0.05 | 0.01 | 0.22 | 0.00 | 0.16 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 |
| SLC4A5 | ENSG00000188687 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.13 | 0.00 | 0.04 | 0.00 | 0.07 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.17 | 0.04 | 0.03 | 0.00 | 0.06 | 0.01 | 0.10 | 0.02 | 0.06 | 0.05 | 0.04 | 0.05 | 0.00 | 0.00 | 0.04 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| CILP | ENSG00000138615 | 0.01 | 0.00 | 0.00 | 0.00 | 0.14 | 0.00 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.08 | 0.04 | 0.02 | 0.02 | 0.05 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.03 | 0.03 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.12 | 0.11 | 0.05 | 0.01 | 0.01 | 0.04 | 0.00 | 0.17 | 0.06 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 |
| CPS1 | ENSG00000021826 | 0.02 | 0.05 | 0.04 | 0.03 | 0.00 | 0.03 | 0.02 | 0.04 | 0.02 | 0.21 | 0.00 | 0.00 | 0.00 | 0.12 | 0.03 | 0.02 | 0.05 | 0.14 | 0.03 | 0.17 | 0.06 | 0.11 | 0.07 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.08 | 0.02 | 0.08 | 0.08 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.20 | 0.13 | 0.02 | 0.30 | 0.03 | 0.04 | 0.06 | 0.05 | 0.07 | 0.16 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.04 |
| NUP210 | ENSG00000132182 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.48 | 0.01 | 0.00 | 0.03 | 0.03 | 0.06 | 0.02 | 0.05 | 0.02 | 0.03 | 0.03 | 0.02 | 0.05 | 0.02 | 0.05 | 0.05 | 0.02 | 0.03 | 0.03 | 0.06 | 0.01 | 0.02 | 0.07 | 0.01 | 0.00 | 0.18 | 0.08 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.03 | 0.15 | 0.21 | 0.03 | 0.01 | 0.09 | 0.04 | 0.22 | 0.14 | 0.24 | 0.01 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 |
| ABCB4 | ENSG00000005471 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.02 | 0.19 | 0.02 | 0.17 | 0.01 | 0.40 | 0.01 | 0.21 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.08 | 0.00 | 0.08 | 0.02 | 0.04 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.20 | 0.05 | 0.07 | 0.02 | 0.02 | 0.02 | 0.09 | 0.03 | 0.06 | 0.05 | 0.13 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| COL23A1 | ENSG00000050767 | 0.33 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.12 | 0.00 | 0.01 | 0.03 | 0.07 | 0.10 | 0.04 | 0.04 | 0.05 | 0.03 | 0.07 | 0.13 | 0.02 | 0.04 | 0.04 | 0.02 | 0.02 | 0.04 | 0.03 | 0.03 | 0.01 | 0.13 | 0.02 | 0.05 | 0.01 | 0.37 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.10 | 0.04 | 0.24 | 0.14 | 0.03 | 0.04 | 0.05 | 0.02 | 0.22 | 0.02 | 0.17 | 0.09 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.07 | 0.02 | 0.06 | 0.04 | 0.02 | 0.09 | 0.09 |
| CCR7 | ENSG00000126353 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.11 | 0.02 | 0.00 | 0.01 | 0.01 | 0.04 | 0.09 | 0.01 | 0.11 | 0.04 | 0.07 | 0.01 | 0.65 | 0.03 | 0.59 | 0.01 | 0.14 | 0.00 | 0.20 | 0.01 | 0.04 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.01 | 0.17 | 0.00 | 0.12 | 0.00 | 0.00 | 0.27 | 0.08 | 0.04 | 0.16 | 0.05 | 0.04 | 0.08 | 0.07 | 0.26 | 0.09 | 0.07 | 0.13 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.02 | 0.03 |
| CPT1C | ENSG00000169169 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.05 | 0.10 | 0.03 | 0.02 | 0.07 | 0.05 | 0.08 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.03 | 0.03 | 0.00 | 0.07 | 0.25 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.13 | 0.04 | 0.05 | 0.33 | 0.05 | 0.07 | 0.07 | 0.05 | 0.18 | 0.15 | 0.03 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.00 | 0.14 | 0.03 | 0.13 | 0.00 | 0.00 | 0.02 | 0.03 |
| UGT2B4 | ENSG00000156096 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.12 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.03 | 0.23 | 0.01 | 0.08 | 0.02 | 0.13 | 0.01 | 0.03 | 0.02 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.04 | 0.07 | 0.00 | 0.03 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.26 | 0.08 | 0.04 | 0.03 | 0.04 | 0.01 | 0.06 | 0.05 | 0.07 | 0.06 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 |
| MYLK2 | ENSG00000101306 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.31 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.10 | 0.01 | 0.28 | 0.00 | 0.16 | 0.00 | 0.08 | 0.00 | 0.06 | 0.00 | 0.17 | 0.00 | 0.22 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.28 | 0.02 | 0.23 | 0.00 | 0.17 | 0.00 | 1.27 | 0.00 | 0.13 | 0.02 | 0.18 | 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 |
| IL4I1 | ENSG00000104951 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.06 | 0.10 | 0.03 | 0.02 | 0.07 | 0.03 | 0.07 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.03 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.04 | 0.04 | 0.32 | 0.05 | 0.07 | 0.04 | 0.06 | 0.11 | 0.15 | 0.03 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.10 | 0.06 | 0.00 | 0.14 | 0.02 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| CASP8 | ENSG00000064012 | 0.03 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.17 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.02 | 0.15 | 0.09 | 0.10 | 0.11 | 0.11 | 0.06 | 0.07 | 0.04 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.27 | 0.09 | 0.09 | 0.18 | 0.05 | 0.02 | 0.06 | 0.05 | 0.06 | 0.11 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.04 |
| SDC2 | ENSG00000169439 | 0.00 | 0.00 | 0.01 | 0.00 | 0.14 | 0.00 | 0.08 | 0.01 | 0.31 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.18 | 0.01 | 0.18 | 0.01 | 0.10 | 0.00 | 0.21 | 0.01 | 0.15 | 0.00 | 0.08 | 0.01 | 0.18 | 0.00 | 0.04 | 0.01 | 0.28 | 0.00 | 0.25 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.38 | 0.00 | 0.52 | 0.07 | 0.11 | 0.00 | 0.10 | 0.01 | 0.38 | 0.02 | 0.18 | 0.03 | 0.15 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.13 | 0.00 | 0.01 | 0.00 | 0.39 | 0.00 | 0.12 | 0.01 |
| AZU1 | ENSG00000172232 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.14 | 0.05 | 0.00 | 0.03 | 0.10 | 0.04 | 0.09 | 0.03 | 0.16 | 0.01 | 0.15 | 0.04 | 0.18 | 0.05 | 0.08 | 0.01 | 0.06 | 0.02 | 0.09 | 0.00 | 0.07 | 0.02 | 0.14 | 0.04 | 0.03 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.92 | 0.04 | 0.24 | 0.03 | 0.25 | 0.00 | 0.81 | 0.29 | 0.21 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.08 | 0.01 | 0.08 | 0.01 | 0.01 | 0.04 | 0.02 | 0.08 |
| TRIM28 | ENSG00000130726 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.07 | 0.13 | 0.09 | 0.07 | 0.05 | 0.25 | 0.06 | 0.15 | 0.03 | 0.02 | 0.03 | 0.02 | 0.04 | 0.05 | 0.04 | 0.07 | 0.03 | 0.02 | 0.07 | 0.14 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.15 | 0.06 | 0.18 | 0.35 | 0.12 | 0.05 | 0.08 | 0.07 | 0.14 | 0.12 | 0.07 | 0.30 | 0.00 | 0.06 | 0.02 | 0.01 | 0.16 | 0.03 | 0.01 | 0.17 | 0.05 | 0.12 | 0.00 | 0.00 | 0.04 | 0.06 |
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