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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
voltage dependent anion channel 1	ENSG00000213585	VDAC1	chr5:133971915-134005133:-	0.28	0	1	0
gonadotropin releasing hormone receptor 2 (pseudogene)	ENSG00000211451	GNRHR2	chr1:145919013-145925341:+	0.28	0.28	1	2
carbonic anhydrase 4	ENSG00000167434	CA4	chr17:60149936-60170899:+	0.28	0	1	0
transmembrane protein 184A	ENSG00000164855	TMEM184A	chr7:1542235-1560821:-	0.27	0.39	2	1
tumor protein p53 inducible protein 13	ENSG00000167543	TP53I13	chr17:29566052-29573157:+	0.26	0	1	0
GNAS complex locus	ENSG00000087460	GNAS	chr20:58839718-58911192:+	0.26	0	1	0
trans-golgi network protein 2	ENSG00000152291	TGOLN2	chr2:85318020-85328425:-	0.26	0	1	0
integrin subunit alpha 6	ENSG00000091409	ITGA6	chr2:172427354-172506282:+	0.26	0	1	0
lemur tyrosine kinase 2	ENSG00000164715	LMTK2	chr7:98106885-98209633:+	0.26	0	2	0
ArfGAP with dual PH domains 1	ENSG00000105963	ADAP1	chr7:897901-955407:-	0.26	0.4	2	1
G protein-coupled receptor 137B	ENSG00000077585	GPR137B	chr1:236142505-236221865:+	0.26	0	1	0
protein kinase N1	ENSG00000123143	PKN1	chr19:14433053-14471867:+	0.26	0	1	0
ORAI calcium release-activated calcium modulator 3	ENSG00000175938	ORAI3	chr16:30949066-30956461:+	0.26	0	2	0
transmembrane protein 150A	ENSG00000168890	TMEM150A	chr2:85598548-85603196:-	0.26	0	1	0
gamma-glutamyl carboxylase	ENSG00000115486	GGCX	chr2:85544723-85561547:-	0.26	0	1	0
CLPTM1 regulator of GABA type A receptor forward trafficking	ENSG00000104853	CLPTM1	chr19:44954585-44993341:+	0.25	0.46	1	2
TraB domain containing 2A	ENSG00000186854	TRABD2A	chr2:84821650-84907008:-	0.25	0	1	0
CD83 molecule	ENSG00000112149	CD83	chr6:14117256-14136918:+	0.25	0	1	0
platelet derived growth factor receptor alpha	ENSG00000134853	PDGFRA	chr4:54229097-54298247:+	0.25	0	1	0
pecanex 2	ENSG00000135749	PCNXL2	chr1:232983435-233295713:-	0.25	0.24	1	1

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