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).

 

Summary of the G-score of the putative cancer-causing GESPs driven by SCNAs in each cancer type


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ACCBLCABRCACESCCHOLCOADDLBCESCAGBMHNSCKICHKIRCKIRPLAMLLGGLIHCLUADLUSCMESOOVPAADPCPGPRADREADSARCSKCMSTADTGCTTHCATHYMUCECUCSUVM
 HGNC Name  Ensembl Gene ID  HGNC Symbol  Genomic Location  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del 
programmed cell death 1ENSG00000188389PDCD1chr2:241849881-241858908:-              0.32                                                                                                                                                                                                                                                          
fms related receptor tyrosine kinase 3 ligandENSG00000090554FLT3LGchr19:49474207-49486231:+                                                                                                                                                              0.31                                                                                                          
ankyrin repeat and sterile alpha motif domain containing 1BENSG00000185046ANKS1Bchr12:98726457-99984654:-                                                                                                                                                              0.31                                                                                                          
gap junction protein alpha 3ENSG00000121743GJA3chr13:20138255-20161049:-                                                                              0.18                                                                0.14                                                                                                                          
Fas cell surface death receptorENSG00000026103FASchr10:88990531-89015785:+                                                                                                                                                              0.31                                                                                                          
tetraspanin 2ENSG00000134198TSPAN2chr1:115048011-115089500:-                                                                                                                                      0.14        0.17                                                                                                                          
CD81 moleculeENSG00000110651CD81chr11:2376177-2397419:+                                                              0.15                                                                                0.16                                                                                                                          
sortilin related VPS10 domain containing receptor 1ENSG00000108018SORCS1chr10:106573663-107164534:-                                                                                                                                                              0.3                                                                                                          
podoplaninENSG00000162493PDPNchr1:13583465-13617957:+                      0.19                                                                                                                        0.11                                                                                                                          
sorbin and SH3 domain containing 1ENSG00000095637SORBS1chr10:95311771-95561414:-                                                                                                                                                              0.3                                                                                                          
interferon induced transmembrane protein 1ENSG00000185885IFITM1chr11:313506-315272:+                      0.14                                                                                                                        0.16                                                                                                                          
protein tyrosine phosphatase non-receptor type 22ENSG00000134242PTPN22chr1:113813811-113871759:-                                                                              0.15                                                        0.14                                                                                                                                  
beta-2-microglobulinENSG00000166710B2Mchr15:44711477-44718877:+                                                                                                                                              0.12                                                                0.17                                                          
LY6/PLAUR domain containing 5ENSG00000159871LYPD5chr19:43795929-43827206:-                                                                                                                                                              0.29                                                                                                          
CEA cell adhesion molecule 19ENSG00000186567CEACAM19chr19:44662278-44684359:+                                                                                                                                                              0.29                                                                                                          
solute carrier family 16 member 1ENSG00000155380SLC16A1chr1:112911847-112957013:-                                                                              0.15                                                        0.14                                                                                                                                  
basal cell adhesion molecule (Lutheran blood group)ENSG00000187244BCAMchr19:44809059-44821420:+                                                                                                                                                              0.29                                                                                                          
plasminogen activator, urokinase receptorENSG00000011422PLAURchr19:43646095-43670547:-                                                                                                                                                              0.28                                                                                                          
protein kinase C and casein kinase substrate in neurons 2ENSG00000100266PACSIN2chr22:42835412-43015145:-                                                                                                                                                                                                                                                              0.28          
FER tyrosine kinaseENSG00000151422FERchr5:108747822-109196841:+                                                              0.13                                                                                                                                                        0.15                                                  

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