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 
consortin, connexin sorting proteinENSG00000162852CNSTchr1:246566444-246668584:+  0.89    0.25    4    1  
solute carrier family 52 member 2ENSG00000185803SLC52A2chr8:144354135-144361272:+  0.88    0    3    0  
solute carrier family 39 member 4ENSG00000147804SLC39A4chr8:144409742-144416895:-  0.88    0    3    0  
protein phosphatase 1 regulatory subunit 16AENSG00000160972PPP1R16Achr8:144477969-144502121:+  0.88    0    3    0  
VPS28 subunit of ESCRT-IENSG00000160948VPS28chr8:144423601-144428563:-  0.88    0    3    0  
LanC like 2ENSG00000132434LANCL2chr7:55365448-55433742:+  0.87    0    3    0  
transmembrane protein 8BENSG00000137103TMEM8Bchr9:35814451-35854847:+  0.87    0    3    0  
serine peptidase inhibitor, Kunitz type 2ENSG00000167642SPINT2chr19:38244035-38292614:+  0.86    0    2    0  
potassium two pore domain channel subfamily K member 6ENSG00000099337KCNK6chr19:38319844-38332076:+  0.86    0    2    0  
cytohesin 1ENSG00000108669CYTH1chr17:78674048-78782297:-  0.86    0    4    0  
programmed cell death 1 ligand 2ENSG00000197646PDCD1LG2chr9:5510570-5571254:+  0.86    0    4    0  
major facilitator superfamily domain containing 11ENSG00000092931MFSD11chr17:76735865-76781449:+  0.85    0    4    0  
Rac family small GTPase 3ENSG00000169750RAC3chr17:82031624-82034204:+  0.84    0.11    4    1  
ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1ENSG00000186635ARAP1chr11:72685069-72793599:-  0.84    0.1    1    1  
solute carrier family 20 member 2ENSG00000168575SLC20A2chr8:42416475-42541926:-  0.83    0    3    0  
solute carrier family 44 member 2ENSG00000129353SLC44A2chr19:10602457-10644559:+  0.83    0    1    0  
major facilitator superfamily domain containing 2AENSG00000168389MFSD2Achr1:39955112-39969968:+  0.82    0    3    0  
cysteine rich hydrophobic domain 2ENSG00000109220CHIC2chr4:54009789-54064690:-  0.82    0    3    0  
solute carrier family 47 member 1ENSG00000142494SLC47A1chr17:19495385-19579034:+  0.81    0    2    0  
CD44 molecule (Indian blood group)ENSG00000026508CD44chr11:35138870-35232402:+  0.8    0    4    0  

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