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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
ectonucleotide pyrophosphatase/phosphodiesterase 1	ENSG00000197594	ENPP1	chr6:131808016-131895155:+	0	0.46	0	4
myoferlin	ENSG00000138119	MYOF	chr10:93306429-93482317:-	0	0.46	0	2
gap junction protein beta 2	ENSG00000165474	GJB2	chr13:20187470-20192898:-	0	0.46	0	3
nectin cell adhesion molecule 1	ENSG00000110400	PVRL1	chr11:119623408-119729084:-	0	0.44	0	2
protein kinase N2	ENSG00000065243	PKN2	chr1:88684222-88836255:+	0	0.44	0	2
tetraspanin 4	ENSG00000214063	TSPAN4	chr11:842808-867116:+	0	0.44	0	3
signal peptide peptidase like 3	ENSG00000157837	SPPL3	chr12:120762510-120904371:-	0	0.44	0	2
ADAM metallopeptidase domain 8	ENSG00000151651	ADAM8	chr10:133262403-133276868:-	0	0.43	0	3
semaphorin 4G	ENSG00000095539	SEMA4G	chr10:100969518-100985871:+	0	0.43	0	2
KN motif and ankyrin repeat domains 1	ENSG00000107104	KANK1	chr9:470291-746106:+	0	0.43	0	2
interferon induced protein with tetratricopeptide repeats 5	ENSG00000152778	IFIT5	chr10:89414586-89421001:+	0	0.43	0	2
erythrocyte membrane protein band 4.1	ENSG00000159023	EPB41	chr1:28887091-29120046:+	0	0.42	0	2
RAB11 family interacting protein 2	ENSG00000107560	RAB11FIP2	chr10:118004916-118046603:-	0	0.42	0	3
major facilitator superfamily domain containing 4B	ENSG00000173214	KIAA1919	chr6:111259348-111271167:+	0	0.42	0	3
sidekick cell adhesion molecule 1	ENSG00000146555	SDK1	chr7:3301448-4269000:+	0	0.42	0	1
phospholipid phosphatase 2	ENSG00000141934	PPAP2C	chr19:281040-291504:-	0	0.42	0	3
neuralized E3 ubiquitin protein ligase 1	ENSG00000107954	NEURL1	chr10:103493979-103592552:+	0	0.42	0	2
toll interacting protein	ENSG00000078902	TOLLIP	chr11:1274371-1309654:-	0	0.42	0	3
collagen type VI alpha 3 chain	ENSG00000163359	COL6A3	chr2:237324003-237414375:-	0	0.42	0	2
lymphocyte cytosolic protein 1	ENSG00000136167	LCP1	chr13:46125920-46211871:-	0	0.41	0	1

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