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 |
| erb-b2 receptor tyrosine kinase 2 | ENSG00000141736 | ERBB2 | chr17:39687914-39730426:+ | 5.86 | 0 | 11 | 0 |
| growth factor receptor bound protein 7 | ENSG00000141738 | GRB7 | chr17:39737927-39747291:+ | 5.35 | 0 | 10 | 0 |
| anoctamin 1 | ENSG00000131620 | ANO1 | chr11:70078302-70189528:+ | 4.28 | 0 | 3 | 0 |
| Fas associated via death domain | ENSG00000168040 | FADD | chr11:70203163-70207390:+ | 4.27 | 0.11 | 3 | 1 |
| fibroblast growth factor receptor substrate 2 | ENSG00000166225 | FRS2 | chr12:69470349-69579789:+ | 3.34 | 0 | 9 | 0 |
| epidermal growth factor receptor | ENSG00000146648 | EGFR | chr7:55019021-55256620:+ | 3.05 | 0 | 7 | 0 |
| CDC42 small effector 1 | ENSG00000197622 | CDC42SE1 | chr1:151050971-151070325:- | 3.05 | 0 | 11 | 0 |
| histocompatibility minor 13 | ENSG00000101294 | HM13 | chr20:31514428-31577923:+ | 3 | 0 | 8 | 0 |
| zinc finger DHHC-type containing 11 | ENSG00000188818 | ZDHHC11 | chr5:795606-850986:- | 2.81 | 0 | 9 | 0 |
| tetraspanin 31 | ENSG00000135452 | TSPAN31 | chr12:57738013-57750211:+ | 2.65 | 0 | 5 | 0 |
| ceramide synthase 2 | ENSG00000143418 | CERS2 | chr1:150960583-150975004:- | 2.61 | 0 | 10 | 0 |
| phosphatidylinositol-4-phosphate 5-kinase type 1 alpha | ENSG00000143398 | PIP5K1A | chr1:151197949-151249536:+ | 2.46 | 0 | 9 | 0 |
| solute carrier family 12 member 7 | ENSG00000113504 | SLC12A7 | chr5:1050376-1112035:- | 2.39 | 0.13 | 9 | 1 |
| CLPTM1 like | ENSG00000049656 | CLPTM1L | chr5:1317744-1345099:- | 2.32 | 0.13 | 9 | 1 |
| solute carrier family 39 member 1 | ENSG00000143570 | SLC39A1 | chr1:153959099-153968184:- | 1.94 | 0 | 7 | 0 |
| TM2 domain containing 3 | ENSG00000184277 | TM2D3 | chr15:101621444-101652391:- | 1.83 | 0 | 8 | 0 |
| insulin like growth factor 1 receptor | ENSG00000140443 | IGF1R | chr15:98648971-98964530:+ | 1.76 | 0 | 7 | 0 |
| transmembrane 9 superfamily member 4 | ENSG00000101337 | TM9SF4 | chr20:32109506-32167258:+ | 1.72 | 0 | 2 | 0 |
| lysosomal associated membrane protein 1 | ENSG00000185896 | LAMP1 | chr13:113297241-113323672:+ | 1.64 | 0 | 7 | 0 |
| transmembrane and coiled-coil domains 3 | ENSG00000150403 | TMCO3 | chr13:113490995-113554590:+ | 1.62 | 0 | 7 | 0 |
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