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 |
| MMP3 | ENSG00000149968 | 0.25 | 0.00 | 1 | 0 |
| OR8K1 | ENSG00000150261 | 0.00 | 0.00 | 0 | 0 |
| OR5M9 | ENSG00000150269 | 0.00 | 0.00 | 0 | 0 |
| CTF1 | ENSG00000150281 | 0.86 | 0.00 | 2 | 0 |
| FCGR1A | ENSG00000150337 | 0.00 | 0.00 | 0 | 0 |
| HNMT | ENSG00000150540 | 0.00 | 0.20 | 0 | 1 |
| PDCD4 | ENSG00000150593 | 0.00 | 0.10 | 0 | 1 |
| ADRA2A | ENSG00000150594 | 0.00 | 0.00 | 0 | 0 |
| CNDP1 | ENSG00000150656 | 0.00 | 0.00 | 0 | 0 |
| IL18 | ENSG00000150782 | 0.00 | 0.66 | 0 | 4 |
| PRSS53 | ENSG00000151006 | 0.00 | 0.00 | 0 | 0 |
| SLC7A11 | ENSG00000151012 | 0.00 | 0.00 | 0 | 0 |
| LYZL2 | ENSG00000151033 | 0.00 | 0.00 | 0 | 0 |
| KCNA6 | ENSG00000151079 | 0.00 | 0.00 | 0 | 0 |
| EIF4E | ENSG00000151247 | 0.00 | 0.00 | 0 | 0 |
| ATP6V1G3 | ENSG00000151418 | 0.00 | 0.00 | 0 | 0 |
| QDPR | ENSG00000151552 | 0.00 | 0.00 | 0 | 0 |
| AKR1C2 | ENSG00000151632 | 0.00 | 0.00 | 0 | 0 |
| ADAM8 | ENSG00000151651 | 0.00 | 0.43 | 0 | 3 |
| ITIH2 | ENSG00000151655 | 0.00 | 0.00 | 0 | 0 |
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