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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
GTP binding protein overexpressed in skeletal muscle	ENSG00000164949	GEM	chr8:94249253-94262350:-	0.52	0	2	0
phospholipid phosphatase 5	ENSG00000147535	PPAPDC1B	chr8:38263130-38269243:-	0.52	0	3	0
solute carrier family 26 member 1	ENSG00000145217	SLC26A1	chr4:979073-993440:-	0.52	0	2	0
MET proto-oncogene, receptor tyrosine kinase	ENSG00000105976	MET	chr7:116672390-116798386:+	0.52	0	3	0
syndecan binding protein	ENSG00000137575	SDCBP	chr8:58552924-58582860:+	0.52	0	3	0
carbonic anhydrase 9	ENSG00000107159	CA9	chr9:35673856-35681159:+	0.52	0	2	0
ephrin A3	ENSG00000143590	EFNA3	chr1:155078872-155087538:+	0.52	0	3	0
nicastrin	ENSG00000162736	NCSTN	chr1:160343272-160358952:+	0.51	0	3	0
proteolipid protein 2	ENSG00000102007	PLP2	chrX:49171926-49175239:+	0.49	0	1	0
potassium voltage-gated channel subfamily E regulatory subunit 3	ENSG00000175538	KCNE3	chr11:74454841-74467729:-	0.49	0	1	0
glycerophosphodiester phosphodiesterase domain containing 5	ENSG00000158555	GDPD5	chr11:75434640-75525903:-	0.49	0	1	0
ATP binding cassette subfamily C member 4	ENSG00000125257	ABCC4	chr13:95019829-95301446:-	0.48	0	3	0
rhomboid 5 homolog 2	ENSG00000129667	RHBDF2	chr17:76470891-76501790:-	0.48	0	2	0
solute carrier family 6 member 12	ENSG00000111181	SLC6A12	chr12:190077-214570:-	0.47	0	1	0
podocalyxin like	ENSG00000128567	PODXL	chr7:131500262-131558217:-	0.46	0	1	0
F11 receptor	ENSG00000158769	F11R	chr1:160995211-161021348:-	0.46	0	2	0
alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B	ENSG00000167889	MGAT5B	chr17:76868456-76950393:+	0.45	0	2	0
opsin 3	ENSG00000054277	OPN3	chr1:241590102-241677376:-	0.45	0	2	0
ADAMTS like 4	ENSG00000143382	ADAMTSL4	chr1:150549369-150560937:+	0.45	0	1	0
ephrin B2	ENSG00000125266	EFNB2	chr13:106489731-106535114:-	0.45	0	3	0

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