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 |
| VN2R1P | ENSG00000174930 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.13 | 0.01 | 0.89 | 0.01 | 0.47 | 0.00 | 0.60 | 0.02 | 0.15 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.08 | 0.01 | 0.03 | 0.01 | 0.10 | 0.01 | 0.00 | 0.07 | 0.00 | 0.00 | 0.14 | 0.01 | 0.72 | 0.02 | 0.47 | 0.01 | 0.17 | 0.01 | 0.21 | 0.02 | 0.05 | 0.08 | 0.10 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 |
| OR5M3 | ENSG00000174937 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.02 | 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 |
| P2RY14 | ENSG00000174944 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.10 | 0.02 | 0.86 | 0.01 | 0.44 | 0.00 | 0.53 | 0.02 | 0.11 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.08 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.16 | 0.01 | 0.69 | 0.02 | 0.41 | 0.01 | 0.16 | 0.01 | 0.23 | 0.07 | 0.06 | 0.09 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| GPR171 | ENSG00000174946 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.10 | 0.02 | 0.86 | 0.01 | 0.44 | 0.00 | 0.53 | 0.02 | 0.11 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.08 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.15 | 0.01 | 0.69 | 0.02 | 0.41 | 0.01 | 0.16 | 0.01 | 0.23 | 0.07 | 0.06 | 0.09 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| GPR149 | ENSG00000174948 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.11 | 0.01 | 0.88 | 0.00 | 0.45 | 0.00 | 0.57 | 0.03 | 0.13 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.08 | 0.01 | 0.03 | 0.03 | 0.10 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.14 | 0.01 | 0.69 | 0.02 | 0.41 | 0.01 | 0.16 | 0.01 | 0.21 | 0.02 | 0.05 | 0.10 | 0.10 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 |
| CD164L2 | ENSG00000174950 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.09 | 0.00 | 0.01 | 0.05 | 0.19 | 0.04 | 0.06 | 0.03 | 0.10 | 0.02 | 0.07 | 0.04 | 0.13 | 0.02 | 0.13 | 0.00 | 0.17 | 0.00 | 0.24 | 0.00 | 0.10 | 0.00 | 0.21 | 0.00 | 1.06 | 0.04 | 0.04 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.18 | 0.10 | 0.44 | 0.04 | 0.08 | 0.04 | 0.12 | 0.03 | 0.18 | 0.12 | 0.08 | 0.04 | 0.04 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.02 | 0.02 | 0.07 | 0.00 | 0.09 | 0.07 | 0.06 |
| FUT1 | ENSG00000174951 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.08 | 0.04 | 0.10 | 0.02 | 0.02 | 0.07 | 0.05 | 0.08 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.05 | 0.03 | 0.00 | 0.07 | 0.21 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.04 | 0.33 | 0.05 | 0.07 | 0.03 | 0.06 | 0.19 | 0.22 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.00 | 0.13 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.03 |
| OR5J2 | ENSG00000174957 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.03 | 0.13 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.03 | 0.08 | 0.03 | 0.11 | 0.01 | 0.16 | 0.05 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.12 | 0.06 | 0.04 | 0.02 | 0.04 | 0.03 | 0.34 | 0.03 | 0.10 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.05 | 0.04 |
| OR10AG1 | ENSG00000174970 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.03 | 0.13 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.03 | 0.08 | 0.03 | 0.11 | 0.01 | 0.16 | 0.05 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.12 | 0.06 | 0.04 | 0.02 | 0.04 | 0.03 | 0.34 | 0.03 | 0.10 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.05 | 0.04 |
| OR4S2 | ENSG00000174982 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.03 | 0.13 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.03 | 0.08 | 0.03 | 0.11 | 0.01 | 0.16 | 0.05 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.12 | 0.06 | 0.04 | 0.02 | 0.04 | 0.03 | 0.34 | 0.03 | 0.10 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.05 | 0.04 |
| ZG16 | ENSG00000174992 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.08 | 0.01 | 0.03 | 0.01 | 0.08 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.07 | 0.03 | 0.02 | 0.02 | 0.08 | 0.01 | 0.34 | 0.05 | 0.04 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| SLC22A1 | ENSG00000175003 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.02 | 0.08 | 0.00 | 0.02 | 0.00 | 0.18 | 0.02 | 0.07 | 0.07 | 0.05 | 0.03 | 0.04 | 0.09 | 0.05 | 0.06 | 0.07 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.03 | 0.02 | 0.12 | 0.00 | 0.18 | 0.14 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.12 | 0.07 | 0.44 | 0.00 | 0.10 | 0.03 | 0.04 | 0.08 | 0.05 | 0.19 | 0.06 | 0.01 | 0.05 | 0.00 | 0.00 | 0.06 | 0.02 | 0.00 | 0.05 | 0.00 | 0.11 | 0.06 | 0.06 | 0.01 | 0.15 |
| CHST2 | ENSG00000175040 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.07 | 0.01 | 0.54 | 0.01 | 0.30 | 0.00 | 0.36 | 0.01 | 0.11 | 0.01 | 0.01 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.10 | 0.02 | 0.54 | 0.02 | 0.32 | 0.01 | 0.11 | 0.00 | 0.24 | 0.02 | 0.06 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.04 |
| PDIK1L | ENSG00000175087 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.09 | 0.00 | 0.01 | 0.05 | 0.19 | 0.04 | 0.07 | 0.04 | 0.12 | 0.02 | 0.07 | 0.01 | 0.14 | 0.02 | 0.14 | 0.00 | 0.17 | 0.00 | 0.22 | 0.01 | 0.10 | 0.01 | 0.21 | 0.00 | 1.06 | 0.01 | 0.10 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.18 | 0.09 | 0.44 | 0.04 | 0.07 | 0.02 | 0.13 | 0.14 | 0.18 | 0.14 | 0.09 | 0.04 | 0.06 | 0.02 | 0.00 | 0.00 | 0.11 | 0.00 | 0.02 | 0.02 | 0.08 | 0.00 | 0.09 | 0.05 | 0.06 |
| RAG2 | ENSG00000175097 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.09 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 | 0.06 | 0.01 | 0.12 | 0.02 | 0.12 | 0.00 | 0.19 | 0.02 | 0.12 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.05 | 0.04 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.13 | 0.02 | 0.15 | 0.07 | 0.16 | 0.02 | 0.02 | 0.03 | 0.04 | 0.04 | 0.10 | 0.08 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.02 |
| WFDC5 | ENSG00000175121 | 0.01 | 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 | 0.04 | 0.05 | 0.08 | 0.01 | 0.01 | 0.02 | 0.11 | 0.00 | 0.20 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.02 | 0.24 | 0.05 | 0.04 | 0.05 | 0.11 | 0.01 | 0.39 | 0.00 | 0.11 | 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 | 0.06 | 0.01 |
| OR2T1 | ENSG00000175143 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.04 | 0.14 | 0.04 | 0.02 | 0.02 | 0.08 | 0.05 | 0.13 | 0.01 | 0.17 | 0.03 | 0.10 | 0.02 | 0.27 | 0.04 | 0.13 | 0.01 | 0.04 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.20 | 0.02 | 0.23 | 0.02 | 0.10 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.29 | 0.02 | 0.48 | 0.12 | 0.13 | 0.01 | 0.12 | 0.02 | 0.32 | 0.00 | 0.09 | 0.24 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.24 | 0.02 |
| INHBC | ENSG00000175189 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.17 | 0.01 | 0.03 | 0.01 | 0.04 | 0.02 | 0.11 | 0.04 | 0.11 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.07 | 0.01 | 0.06 | 0.01 | 0.40 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.14 | 0.04 | 0.03 | 0.00 | 0.03 | 0.01 | 0.10 | 0.06 | 0.44 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.16 | 0.02 | 0.40 | 0.04 | 0.00 | 0.00 | 0.12 | 0.02 |
| NPPA | ENSG00000175206 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.05 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.07 | 0.05 | 0.05 | 0.11 | 0.04 | 0.08 | 0.16 | 0.08 | 0.10 | 0.08 | 0.01 | 0.13 | 0.00 | 0.20 | 0.03 | 0.06 | 0.03 | 0.23 | 0.00 | 1.07 | 0.04 | 0.13 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.19 | 0.21 | 0.36 | 0.04 | 0.10 | 0.07 | 0.10 | 0.08 | 0.25 | 0.19 | 0.19 | 0.08 | 0.09 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.07 | 0.12 | 0.00 | 0.07 | 0.06 | 0.11 |
| CCNE2 | ENSG00000175305 | 0.00 | 0.00 | 0.02 | 0.00 | 0.14 | 0.00 | 0.07 | 0.02 | 0.25 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.15 | 0.01 | 0.17 | 0.02 | 0.09 | 0.01 | 0.19 | 0.01 | 0.16 | 0.00 | 0.09 | 0.00 | 0.17 | 0.03 | 0.04 | 0.01 | 0.25 | 0.01 | 0.19 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.41 | 0.00 | 0.50 | 0.07 | 0.09 | 0.00 | 0.11 | 0.02 | 0.25 | 0.02 | 0.16 | 0.04 | 0.16 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.09 | 0.00 | 0.02 | 0.01 | 0.39 | 0.00 | 0.11 | 0.01 |
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