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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
zinc and ring finger 3	ENSG00000183579	ZNRF3	chr22:28883592-29057487:+	0	0.67	0	1
plexin B1	ENSG00000164050	PLXNB1	chr3:48403854-48430051:-	0	0.67	0	4
microtubule associated protein 4	ENSG00000047849	MAP4	chr3:47850690-48089272:-	0	0.66	0	4
agrin	ENSG00000188157	AGRN	chr1:1020123-1056118:+	0	0.66	0	3
solute carrier family 23 member 3	ENSG00000213901	SLC23A3	chr2:219161465-219170095:-	0	0.66	0	3
PX domain containing serine/threonine kinase like	ENSG00000168297	PXK	chr3:58332880-58426126:+	0	0.66	0	4
cell adhesion molecule 1	ENSG00000182985	CADM1	chr11:115169218-115504957:-	0	0.66	0	3
layilin	ENSG00000204381	LAYN	chr11:111540280-111561745:+	0	0.65	0	3
fibronectin type III domain containing 10	ENSG00000228594	C1orf233	chr1:1598012-1600096:-	0	0.65	0	4
dopamine receptor D4	ENSG00000069696	DRD4	chr11:637293-640706:+	0	0.65	0	2
junctional adhesion molecule 3	ENSG00000166086	JAM3	chr11:134068925-134152001:+	0	0.65	0	3
oligodendrocyte myelin glycoprotein	ENSG00000126861	OMG	chr17:31272013-31297539:-	0	0.64	0	2
ATPase Na+/K+ transporting subunit alpha 1	ENSG00000163399	ATP1A1	chr1:116372668-116410261:+	0	0.64	0	4
myelin protein zero like 3	ENSG00000160588	MPZL3	chr11:118226690-118252350:-	0	0.64	0	3
delta like canonical Notch ligand 1	ENSG00000198719	DLL1	chr6:170282206-170306565:-	0	0.63	0	2
zinc finger FYVE-type containing 27	ENSG00000155256	ZFYVE27	chr10:97737121-97760907:+	0	0.62	0	3
synaptosome associated protein 23	ENSG00000092531	SNAP23	chr15:42491233-42545356:+	0	0.62	0	3
major facilitator superfamily domain containing 14A	ENSG00000156875	HIAT1	chr1:100038097-100083377:+	0	0.62	0	3
transmembrane 9 superfamily member 3	ENSG00000077147	TM9SF3	chr10:96518109-96587452:-	0	0.62	0	3
calcium homeostasis modulator family member 2	ENSG00000138172	CALHM2	chr10:103446786-103452402:-	0	0.61	0	3

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