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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
par-6 family cell polarity regulator gamma	ENSG00000178184	PARD6G	chr18:80157232-80247546:-	0	1.61	0	9
alkaline phosphatase, biomineralization associated	ENSG00000162551	ALPL	chr1:21509372-21578412:+	0	1.59	0	4
plexin B2	ENSG00000196576	PLXNB2	chr22:50274979-50307627:-	0	1.57	0	7
lipase maturation factor 2	ENSG00000100258	LMF2	chr22:50502949-50507691:-	0	1.57	0	7
G protein-coupled receptor 157	ENSG00000180758	GPR157	chr1:9100305-9129170:-	0	1.51	0	4
solute carrier family 2 member 5	ENSG00000142583	SLC2A5	chr1:9035107-9088478:-	0	1.5	0	3
FAT atypical cadherin 1	ENSG00000083857	FAT1	chr4:186587783-186726722:-	0	1.49	0	7
amyloid beta precursor like protein 2	ENSG00000084234	APLP2	chr11:130069837-130144811:+	0	1.42	0	7
interferon induced transmembrane protein 3	ENSG00000142089	IFITM3	chr11:319669-327537:-	0	1.39	0	6
TNF receptor superfamily member 1B	ENSG00000028137	TNFRSF1B	chr1:12167003-12209228:+	0	1.39	0	3
chromosome 1 open reading frame 159	ENSG00000131591	C1orf159	chr1:1081818-1116361:-	0	1.35	0	7
G protein-coupled receptor 35	ENSG00000178623	GPR35	chr2:240605431-240631259:+	0	1.33	0	6
TNF receptor superfamily member 10c	ENSG00000173535	TNFRSF10C	chr8:23084355-23117437:+	0	1.28	0	8
solute carrier family 30 member 5	ENSG00000145740	SLC30A5	chr5:69093646-69131069:+	0	1.23	0	4
solute carrier family 45 member 1	ENSG00000162426	SLC45A1	chr1:8317826-8344167:+	0	1.22	0	2
single Ig and TIR domain containing	ENSG00000185187	SIGIRR	chr11:405716-417455:-	0	1.21	0	5
STT3 oligosaccharyltransferase complex catalytic subunit A	ENSG00000134910	STT3A	chr11:125591712-125625215:+	0	1.21	0	6
G protein-coupled receptor 153	ENSG00000158292	GPR153	chr1:6247346-6260975:-	0	1.2	0	6
solute carrier family 9 member A1	ENSG00000090020	SLC9A1	chr1:27098815-27166981:-	0	1.18	0	5
TNF receptor superfamily member 10b	ENSG00000120889	TNFRSF10B	chr8:23020133-23069179:-	0	1.17	0	7

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