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 
RAB25, member RAS oncogene familyENSG00000132698RAB25chr1:156061160-156070514:+  0.45    0    2    0  
S100 calcium binding protein A6ENSG00000197956S100A6chr1:153534599-153536244:-  0.44    0    2    0  
family with sequence similarity 174 member BENSG00000185442FAM174Bchr15:92617443-92809884:-  0.43    0    2    0  
solute carrier family 38 member 2ENSG00000134294SLC38A2chr12:46358189-46372867:-  0.43    0    1    0  
tweety family member 3ENSG00000136295TTYH3chr7:2631951-2664802:+  0.42    0.39    3    1  
potassium two pore domain channel subfamily K member 1ENSG00000135750KCNK1chr1:233614004-233672512:+  0.42    0.1    2    1  
CD59 molecule (CD59 blood group)ENSG00000085063CD59chr11:33698261-33736445:-  0.42    0    2    0  
dendrocyte expressed seven transmembrane proteinENSG00000164935DCSTAMPchr8:104339087-104356689:+  0.42    0    1    0  
NIPA like domain containing 2ENSG00000104361NIPAL2chr8:98189833-98294393:-  0.42    0    1    0  
regulating synaptic membrane exocytosis 2ENSG00000176406RIMS2chr8:103500748-104256094:+  0.42    0    1    0  
fibroblast growth factor receptor like 1ENSG00000127418FGFRL1chr4:1009936-1026897:+  0.42    0    1    0  
solute carrier family 49 member 3ENSG00000169026MFSD7chr4:681829-689441:-  0.42    0    1    0  
endoplasmic reticulum metallopeptidase 1ENSG00000099219ERMP1chr9:5765076-5833117:-  0.42    0.31    2    2  
multiple C2 and transmembrane domain containing 2ENSG00000140563MCTP2chr15:94231538-94483952:+  0.42    0    2    0  
fibroblast growth factor receptor 1ENSG00000077782FGFR1chr8:38411138-38468834:-  0.41    0    2    0  
oncostatin M receptorENSG00000145623OSMRchr5:38845858-38945596:+  0.41    0    2    0  
receptor interacting serine/threonine kinase 1ENSG00000137275RIPK1chr6:3063991-3115187:+  0.41    0.38    2    2  
synaptic vesicle glycoprotein 2AENSG00000159164SV2Achr1:149903318-149917882:-  0.4    0    2    0  
solute carrier family 4 member 11ENSG00000088836SLC4A11chr20:3227417-3239190:-  0.4    0    2    0  
interleukin 1 receptor accessory proteinENSG00000196083IL1RAPchr3:190514051-190659750:+  0.39    0    2    0  

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