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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).

Pan-cancer level overall G-score of GESPs that recurrently gained or lost copy number in at least one cancer types

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				Overall_Gscore		No. of Cancer Types
HGNC Name	Ensembl Gene ID	HGNC Symbol	Genomic Location	Amplification	Deletion	Amplification	Deletion
very low density lipoprotein receptor	ENSG00000147852	VLDLR	chr9:2621834-2660053:+	0	0.18	0	1
membrane associated ring-CH-type finger 1	ENSG00000145416	1-Mar	chr4:163524298-164384050:-	0	0.18	0	1
dispatched RND transporter family member 2	ENSG00000140323	DISP2	chr15:40358235-40378639:+	0	0.18	0	1
solute carrier family 6 member 20	ENSG00000163817	SLC6A20	chr3:45755450-45796535:-	0	0.18	0	1
nucleoporin 210	ENSG00000132182	NUP210	chr3:13316235-13420309:-	0	0.18	0	1
transient receptor potential cation channel subfamily M member 2	ENSG00000142185	TRPM2	chr21:44350163-44443081:+	0	0.18	0	1
frizzled class receptor 2	ENSG00000180340	FZD2	chr17:44557459-44559570:+	0	0.18	0	1
diacylglycerol lipase alpha	ENSG00000134780	DAGLA	chr11:61680433-61747001:+	0	0.18	0	1
phospholipase C delta 3	ENSG00000161714	PLCD3	chr17:45108967-45133354:-	0	0.18	0	1
solute carrier family 38 member 3	ENSG00000188338	SLC38A3	chr3:50205246-50221486:+	0	0.18	0	1
oxytocin receptor	ENSG00000180914	OXTR	chr3:8750408-8769628:-	0	0.18	0	1
G protein-coupled receptor 39	ENSG00000183840	GPR39	chr2:132416574-132646559:+	0	0.18	0	1
ribosomal protein SA	ENSG00000168028	RPSA	chr3:39406689-39412542:+	0	0.18	0	1
inducible T cell costimulator ligand	ENSG00000160223	ICOSLG	chr21:44222991-44240966:-	0	0.18	0	1
Ig-like domain-containing protein	ENSG00000277117	ICOSLG	chr21:5022493-5040666:+	0	0.18	0	1
gap junction protein beta 6	ENSG00000121742	GJB6	chr13:20221971-20232395:-	0	0.18	0	1
CUB domain containing protein 1	ENSG00000163814	CDCP1	chr3:45082278-45146422:-	0	0.18	0	1
hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2	ENSG00000099822	HCN2	chr19:589893-617159:+	0	0.18	0	1
leukocyte associated immunoglobulin like receptor 1	ENSG00000167613	LAIR1	chr19:54351384-54370558:-	0	0.17	0	1
tweety family member 1	ENSG00000167614	TTYH1	chr19:54415219-54436900:+	0	0.17	0	1

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