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 |
| exocyst complex component 7 | ENSG00000182473 | EXOC7 | chr17:76081017-76121576:- | 1.08 | 0 | 5 | 0 |
| talin 1 | ENSG00000137076 | TLN1 | chr9:35696948-35732395:- | 1.07 | 0.13 | 4 | 1 |
| transmembrane protein 104 | ENSG00000109066 | TMEM104 | chr17:74776483-74839779:+ | 1.07 | 0 | 5 | 0 |
| p21 (RAC1) activated kinase 1 | ENSG00000149269 | PAK1 | chr11:77321707-77474635:- | 1.06 | 0.15 | 3 | 1 |
| natriuretic peptide receptor 2 | ENSG00000159899 | NPR2 | chr9:35792154-35809732:+ | 1.05 | 0 | 4 | 0 |
| solute carrier family 6 member 13 | ENSG00000010379 | SLC6A13 | chr12:220621-262873:- | 1.04 | 0 | 2 | 0 |
| calcium activated nucleotidase 1 | ENSG00000171302 | CANT1 | chr17:78991717-79009867:- | 1.04 | 0 | 5 | 0 |
| ELKS/RAB6-interacting/CAST family member 1 | ENSG00000082805 | ERC1 | chr12:990509-1495933:+ | 1 | 0 | 4 | 0 |
| tetraspanin 9 | ENSG00000011105 | TSPAN9 | chr12:3077355-3286564:+ | 0.95 | 0 | 3 | 0 |
| TUB like protein 3 | ENSG00000078246 | TULP3 | chr12:2877223-2941140:+ | 0.95 | 0 | 4 | 0 |
| lymphocyte antigen 6 family member E | ENSG00000160932 | LY6E | chr8:143017982-143023832:+ | 0.94 | 0 | 3 | 0 |
| DC-STAMP domain containing 2 | ENSG00000163354 | DCST2 | chr1:155018520-155033781:- | 0.94 | 0 | 3 | 0 |
| unc-93 homolog B1, TLR signaling regulator | ENSG00000110057 | UNC93B1 | chr11:67991104-68004982:- | 0.93 | 0 | 3 | 0 |
| scribble planar cell polarity protein | ENSG00000180900 | SCRIB | chr8:143790920-143815379:- | 0.93 | 0 | 3 | 0 |
| neutral cholesterol ester hydrolase 1 | ENSG00000144959 | NCEH1 | chr3:172630249-172711218:- | 0.92 | 0 | 2 | 0 |
| late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 | ENSG00000149357 | LAMTOR1 | chr11:72085895-72103387:- | 0.92 | 0.1 | 1 | 1 |
| B cell receptor associated protein 31 | ENSG00000185825 | BCAP31 | chrX:153700497-153724697:- | 0.92 | 0 | 5 | 0 |
| protein tyrosine kinase 2 | ENSG00000169398 | PTK2 | chr8:140657900-141002216:- | 0.91 | 0 | 3 | 0 |
| mal, T cell differentiation protein 2 (gene/pseudogene) | ENSG00000147676 | MAL2 | chr8:119165034-119245673:+ | 0.91 | 0 | 2 | 0 |
| CD274 molecule | ENSG00000120217 | CD274 | chr9:5450503-5470566:+ | 0.91 | 0.19 | 4 | 1 |
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