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 |
| TTBK1 | ENSG00000146216 | 0.00 | 0.00 | 0 | 0 |
| VAT1L | ENSG00000171724 | 0.00 | 0.00 | 0 | 0 |
| CAPN12 | ENSG00000182472 | 0.54 | 0.00 | 1 | 0 |
| LRRN1 | ENSG00000175928 | 0.00 | 0.00 | 0 | 0 |
| DHRS13 | ENSG00000167536 | 0.27 | 0.00 | 1 | 0 |
| PMP22 | ENSG00000109099 | 0.62 | 0.00 | 1 | 0 |
| FAM3B | ENSG00000183844 | 0.00 | 0.16 | 0 | 1 |
| GPRC5B | ENSG00000167191 | 0.00 | 0.00 | 0 | 0 |
| VCAN | ENSG00000038427 | 0.00 | 0.00 | 0 | 0 |
| DCN | ENSG00000011465 | 0.00 | 0.00 | 0 | 0 |
| WFDC3 | ENSG00000124116 | 0.00 | 0.00 | 0 | 0 |
| SLC35F1 | ENSG00000196376 | 0.00 | 0.13 | 0 | 1 |
| MRGPRF | ENSG00000172935 | 0.00 | 0.00 | 0 | 0 |
| ITPR1 | ENSG00000150995 | 0.00 | 0.00 | 0 | 0 |
| TGFBR3 | ENSG00000069702 | 0.00 | 0.23 | 0 | 2 |
| LAMA5 | ENSG00000130702 | 0.52 | 0.00 | 1 | 0 |
| B2M | ENSG00000166710 | 0.00 | 0.29 | 0 | 2 |
| RABGGTB | ENSG00000137955 | 0.00 | 0.00 | 0 | 0 |
| TESK2 | ENSG00000070759 | 0.00 | 0.00 | 0 | 0 |
| SLC12A5 | ENSG00000124140 | 0.00 | 0.00 | 0 | 0 |
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