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 
prostate stem cell antigenENSG00000167653PSCAchr8:142670308-142682724:+                                                                                                                                                                                                          0.24                                                              
Lck interacting transmembrane adaptor 1ENSG00000203896LIME1chr20:63736283-63739103:+                                                                                                                          0.11                                                                0.13                                                                              
mannose receptor C type 2ENSG00000011028MRC2chr17:62627401-62693597:+                                                                                                                                                                                                  0.24                                                                      
nectin cell adhesion molecule 2ENSG00000130202PVRL2chr19:44846175-44889228:+  0.24                                                                                                                                                            0.3                                                                                                0.17          
PVR cell adhesion moleculeENSG00000073008PVRchr19:44643798-44663583:+  0.24                                                                                                                                                            0.29                                                                                                0.17          
notch receptor 3ENSG00000074181NOTCH3chr19:15159038-15200981:-                                                          0.23                                                                                                                                                                                                              
integrin subunit beta 4ENSG00000132470ITGB4chr17:75721328-75757818:+                          0.23                                                                                                                                                                                                                                              
prostate transmembrane protein, androgen induced 1ENSG00000124225PMEPA1chr20:57648392-57711536:-                                                                                                                                                                                                  0.23                                                                      
neurofibromin 2ENSG00000186575NF2chr22:29603556-29698598:+          0.23                                                                                                                                            0.26                                                                                                                  
sarcoglycan betaENSG00000163069SGCBchr4:52020706-52038482:-                                                                                                                                                                                                  0.23                                                                      
LMBR1 domain containing 2ENSG00000164187LMBRD2chr5:36098412-36151961:-                                                                                                                                  0.23                                                                                                                                      
semaphorin 6AENSG00000092421SEMA6Achr5:116443616-116574934:-                                                                                          0.23                                                                                                                                                                              
potassium voltage-gated channel subfamily C member 3ENSG00000131398KCNC3chr19:50311937-50333515:-  0.23                                                                                                                                                            0.32                                                                                                          
V-set and immunoglobulin domain containing 10 likeENSG00000186806VSIG10Lchr19:51331536-51342124:-  0.23                                                                                                                                                                                                                                                                      
SH3 and multiple ankyrin repeat domains 1ENSG00000161681SHANK1chr19:50661827-50719450:-  0.23                                                                                                                                                                                                                                                                      
interleukin 6 receptorENSG00000160712IL6Rchr1:154405193-154469450:+                                                                                                                                                                                                          0.22                                                              
erb-b2 receptor tyrosine kinase 3ENSG00000065361ERBB3chr12:56079857-56103505:+                                                                                                                                                                                                                                                  0.22                      
phosphoprotein membrane anchor with glycosphingolipid microdomains 1ENSG00000076641PAG1chr8:80967810-81112068:-                                                                                                                                                                                                                                                                  0.22      
lymphocyte antigen 96ENSG00000154589LY96chr8:73991352-74029087:+                                                                                                                                                                                                                                                                  0.22      
junctophilin 1ENSG00000104369JPH1chr8:74234700-74321328:-                                                                                                                                                                                                                                                                  0.22      

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