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 |
| leucine rich repeat and fibronectin type III domain containing 1 | ENSG00000128011 | LRFN1 | chr19:39306568-39315336:- | 0.78 | 0 | 1 | 0 |
| semaphorin 4B | ENSG00000185033 | SEMA4B | chr15:90160604-90229679:+ | 0.77 | 0 | 4 | 0 |
| LDL receptor related protein 5 | ENSG00000162337 | LRP5 | chr11:68312609-68449275:+ | 0.77 | 0 | 1 | 0 |
| prolyl 4-hydroxylase subunit beta | ENSG00000185624 | P4HB | chr17:81843159-81860694:- | 0.77 | 0 | 4 | 0 |
| chromosome 11 open reading frame 24 | ENSG00000171067 | C11orf24 | chr11:68261335-68272001:- | 0.76 | 0.1 | 1 | 1 |
| hyperpolarization activated cyclic nucleotide gated potassium channel 3 | ENSG00000143630 | HCN3 | chr1:155277583-155289848:+ | 0.76 | 0 | 4 | 0 |
| delta like canonical Notch ligand 3 | ENSG00000090932 | DLL3 | chr19:39498895-39508481:+ | 0.76 | 0.11 | 1 | 1 |
| IQ motif containing GTPase activating protein 1 | ENSG00000140575 | IQGAP1 | chr15:90388218-90502243:+ | 0.76 | 0 | 4 | 0 |
| calcium and integrin binding 1 | ENSG00000185043 | CIB1 | chr15:90229975-90234047:- | 0.75 | 0 | 4 | 0 |
| activity regulated cytoskeleton associated protein | ENSG00000198576 | ARC | chr8:142611044-142614472:- | 0.74 | 0 | 2 | 0 |
| adhesion G protein-coupled receptor B1 | ENSG00000181790 | ADGRB1 | chr8:142449430-142545009:+ | 0.74 | 0 | 2 | 0 |
| transmembrane protein 123 | ENSG00000152558 | TMEM123 | chr11:102396332-102470384:- | 0.73 | 0 | 3 | 0 |
| calcium voltage-gated channel subunit alpha1 C | ENSG00000151067 | CACNA1C | chr12:1970786-2697950:+ | 0.73 | 0 | 2 | 0 |
| steroid 5 alpha-reductase 3 | ENSG00000128039 | SRD5A3 | chr4:55346109-55373096:+ | 0.73 | 0 | 3 | 0 |
| solute carrier family 45 member 4 | ENSG00000022567 | SLC45A4 | chr8:141207166-141308305:- | 0.72 | 0 | 2 | 0 |
| clathrin heavy chain | ENSG00000141367 | CLTC | chr17:59619689-59696956:+ | 0.72 | 0.13 | 4 | 1 |
| FCH and double SH3 domains 2 | ENSG00000137478 | FCHSD2 | chr11:72836745-73142261:- | 0.72 | 0.1 | 1 | 1 |
| jagged canonical Notch ligand 2 | ENSG00000184916 | JAG2 | chr14:105140981-105168824:- | 0.7 | 0 | 3 | 0 |
| furin, paired basic amino acid cleaving enzyme | ENSG00000140564 | FURIN | chr15:90868592-90883458:+ | 0.7 | 0 | 4 | 0 |
| SLC9A3 regulator 1 | ENSG00000109062 | SLC9A3R1 | chr17:74748652-74769353:+ | 0.69 | 0 | 3 | 0 |
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