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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| Overall_Gscore | No. of Cancer Types | ||||
| HGNC Symbol | Ensembl Gene ID | Amplification | Deletion | Amplification | Deletion |
| TNFRSF8 | ENSG00000120949 | 0.00 | 0.11 | 0 | 1 |
| HYAL3 | ENSG00000186792 | 0.00 | 0.70 | 0 | 4 |
| PRSS3 | ENSG00000010438 | 0.00 | 0.00 | 0 | 0 |
| OPN3 | ENSG00000054277 | 0.45 | 0.00 | 2 | 0 |
| ADAMTSL1 | ENSG00000178031 | 0.00 | 0.00 | 0 | 0 |
| CX3CL1 | ENSG00000006210 | 0.12 | 0.00 | 1 | 0 |
| MIPEP | ENSG00000027001 | 0.00 | 0.32 | 0 | 2 |
| SLC2A9 | ENSG00000109667 | 0.00 | 0.00 | 0 | 0 |
| ACE2 | ENSG00000130234 | 0.00 | 0.00 | 0 | 0 |
| UPP1 | ENSG00000183696 | 0.00 | 0.00 | 0 | 0 |
| PRKCE | ENSG00000171132 | 0.00 | 0.00 | 0 | 0 |
| TRIB3 | ENSG00000101255 | 0.33 | 0.00 | 1 | 0 |
| STK32A | ENSG00000169302 | 0.00 | 0.00 | 0 | 0 |
| PAK1 | ENSG00000149269 | 1.06 | 0.15 | 3 | 1 |
| SLC24A3 | ENSG00000185052 | 0.00 | 0.00 | 0 | 0 |
| CD276 | ENSG00000103855 | 0.12 | 0.00 | 1 | 0 |
| STK31 | ENSG00000196335 | 0.00 | 0.00 | 0 | 0 |
| PCSK5 | ENSG00000099139 | 0.00 | 0.00 | 0 | 0 |
| PDGFRL | ENSG00000104213 | 0.00 | 0.23 | 0 | 2 |
| LCAT | ENSG00000213398 | 0.32 | 0.47 | 2 | 2 |
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