Copy Number
The putative cancer-associated GESPs 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 Name | Ensembl Gene ID | HGNC Symbol | Genomic Location | Amplification | Deletion | Amplification | Deletion |
| T cell immunoglobulin and mucin domain containing 4 | ENSG00000145850 | TIMD4 | chr5:156919282-156963255:- | 0.31 | 0 | 1 | 0 |
| CD74 molecule | ENSG00000019582 | CD74 | chr5:150401637-150412929:- | 0.3 | 0.14 | 1 | 1 |
| solute carrier family 17 member 9 | ENSG00000101194 | SLC17A9 | chr20:62952647-62969585:+ | 0.3 | 0 | 2 | 0 |
| transmembrane protein 63B | ENSG00000137216 | TMEM63B | chr6:44126914-44155519:+ | 0.3 | 0 | 2 | 0 |
| diaphanous related formin 1 | ENSG00000131504 | DIAPH1 | chr5:141515016-141619055:- | 0.3 | 0.15 | 1 | 1 |
| protocadherin gamma subfamily C, 3 | ENSG00000240184 | PCDHGC3 | chr5:141475947-141512979:+ | 0.3 | 0.15 | 1 | 1 |
| protocadherin gamma subfamily A, 9 | ENSG00000261934 | PCDHGA9 | chr5:141402932-141512979:+ | 0.3 | 0.15 | 1 | 1 |
| protocadherin gamma subfamily A, 6 | ENSG00000253731 | PCDHGA6 | chr5:141373914-141512979:+ | 0.3 | 0.15 | 1 | 1 |
| protocadherin gamma subfamily A, 10 | ENSG00000253846 | PCDHGA10 | chr5:141412987-141512979:+ | 0.3 | 0.15 | 1 | 1 |
| protocadherin gamma subfamily A, 1 | ENSG00000204956 | PCDHGA1 | chr5:141330571-141512981:+ | 0.3 | 0.15 | 1 | 1 |
| protocadherin gamma subfamily B, 7 | ENSG00000254122 | PCDHGB7 | chr5:141417645-141512979:+ | 0.3 | 0 | 1 | 0 |
| solute carrier family 29 member 1 (Augustine blood group) | ENSG00000112759 | SLC29A1 | chr6:44219505-44234151:+ | 0.3 | 0 | 2 | 0 |
| heat shock protein 90 alpha family class B member 1 | ENSG00000096384 | HSP90AB1 | chr6:44246166-44253888:+ | 0.3 | 0 | 2 | 0 |
| protocadherin beta 11 | ENSG00000197479 | PCDHB11 | chr5:141199582-141203779:+ | 0.3 | 0.14 | 1 | 1 |
| protocadherin beta 12 | ENSG00000120328 | PCDHB12 | chr5:141208697-141212571:+ | 0.3 | 0.14 | 1 | 1 |
| protocadherin beta 9 | ENSG00000177839 | PCDHB9 | chr5:141187127-141191541:+ | 0.3 | 0.14 | 1 | 1 |
| protocadherin beta 10 | ENSG00000120324 | PCDHB10 | chr5:141187319-141195642:+ | 0.3 | 0.14 | 1 | 1 |
| protocadherin beta 13 | ENSG00000187372 | PCDHB13 | chr5:141213919-141218979:+ | 0.3 | 0.14 | 1 | 1 |
| protocadherin beta 14 | ENSG00000120327 | PCDHB14 | chr5:141222932-141227759:+ | 0.3 | 0.14 | 1 | 1 |
| STEAP3 metalloreductase | ENSG00000115107 | STEAP3 | chr2:119223831-119265652:+ | 0.3 | 0 | 1 | 0 |
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