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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
sphingosine-1-phosphate receptor 4	ENSG00000125910	S1PR4	chr19:3172346-3180332:+	0	0.14	0	1
ras homolog family member B	ENSG00000143878	RHOB	chr2:20447074-20449445:+	0	0.14	0	1
adrenoceptor beta 2	ENSG00000169252	ADRB2	chr5:148825245-148828687:+	0	0.14	0	1
protocadherin beta 4	ENSG00000081818	PCDHB4	chr5:141121799-141125623:+	0	0.14	0	1
protocadherin beta 3	ENSG00000113205	PCDHB3	chr5:141100473-141152636:+	0	0.14	0	1
protocadherin beta 5	ENSG00000113209	PCDHB5	chr5:141135218-141138625:+	0	0.14	0	1
protocadherin beta 15	ENSG00000113248	PCDHB15	chr5:141245349-141249365:+	0	0.14	0	1
myosin IC	ENSG00000197879	MYO1C	chr17:1464098-1492812:-	0	0.14	0	1
scavenger receptor class F member 1	ENSG00000074660	SCARF1	chr17:1633858-1645747:-	0	0.14	0	1
adhesion G protein-coupled receptor G6	ENSG00000112414	ADGRG6	chr6:142301854-142446266:+	0	0.14	0	1
neuregulin 2	ENSG00000158458	NRG2	chr5:139846779-140043299:-	0	0.14	0	1
leucine rich single-pass membrane protein 1	ENSG00000181016	LSMEM1	chr7:112480853-112491062:+	0	0.14	0	1
protocadherin beta 2	ENSG00000112852	PCDHB2	chr5:141094578-141098703:+	0	0.14	0	1
protocadherin alpha 7	ENSG00000204963	PCDHA7	chr5:140834248-141012344:+	0	0.14	0	1
ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	ENSG00000113532	ST8SIA4	chr5:100806935-100903266:-	0	0.14	0	1
transmembrane 4 L six family member 20	ENSG00000168955	TM4SF20	chr2:227362156-227381995:-	0	0.14	0	1
heparin binding EGF like growth factor	ENSG00000113070	HBEGF	chr5:140332843-140346631:-	0	0.14	0	1
V-set domain containing T cell activation inhibitor 1	ENSG00000134258	VTCN1	chr1:117143587-117210960:-	0	0.14	0	1
claudin 23	ENSG00000253958	CLDN23	chr8:8701938-8704106:+	0	0.14	0	1
immunoglobulin heavy constant alpha 1	ENSG00000211895	IGHA1	chr14:105707118-105708665:-	0	0.14	0	1

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