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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
adiponectin receptor 2	ENSG00000006831	ADIPOR2	chr12:1688574-1788678:+	1.57	0	5	0
fibroblast growth factor receptor 3	ENSG00000068078	FGFR3	chr4:1793307-1808872:+	1.56	0	3	0
ephrin A4	ENSG00000243364	EFNA4	chr1:155063731-155069553:+	1.54	0	6	0
carboxypeptidase M	ENSG00000135678	CPM	chr12:68842197-68971570:-	1.49	0	4	0
RAB13, member RAS oncogene family	ENSG00000143545	RAB13	chr1:153981617-153986358:-	1.41	0	6	0
family with sequence similarity 189 member B	ENSG00000160767	FAM189B	chr1:155247205-155255483:-	1.41	0	5	0
G protein-coupled receptor 160	ENSG00000173890	GPR160	chr3:170037929-170085403:+	1.41	0	4	0
RAS p21 protein activator 3	ENSG00000185989	RASA3	chr13:113977783-114132611:-	1.41	0	6	0
ATPase phospholipid transporting 11A	ENSG00000068650	ATP11A	chr13:112690329-112887168:+	1.38	0	6	0
zinc finger DHHC-type containing 11B	ENSG00000206077	ZDHHC11B	chr5:710360-766952:-	1.37	0	5	0
transmembrane protein 94	ENSG00000177728	KIAA0195	chr17:75441159-75500090:+	1.33	0	6	0
semaphorin 6C	ENSG00000143434	SEMA6C	chr1:151131685-151146664:-	1.31	0	6	0
solute carrier family 26 member 11	ENSG00000181045	SLC26A11	chr17:80219699-80253500:+	1.27	0	5	0
ephrin A1	ENSG00000169242	EFNA1	chr1:155127460-155134857:+	1.25	0	5	0
EFR3 homolog A	ENSG00000132294	EFR3A	chr8:131904088-132013642:+	1.24	0	4	0
G protein-coupled receptor 180	ENSG00000152749	GPR180	chr13:94601903-94634645:+	1.22	0	5	0
GRB2 associated binding protein 2	ENSG00000033327	GAB2	chr11:78215297-78418348:-	1.19	0	3	0
nectin cell adhesion molecule 4	ENSG00000143217	PVRL4	chr1:161070995-161089599:-	1.16	0	2	0
phospholipase D1	ENSG00000075651	PLD1	chr3:171600405-171810950:-	1.15	0	3	0
plexin A3	ENSG00000130827	PLXNA3	chrX:154458281-154477779:+	1.09	0	4	0

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