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 
thyroid stimulating hormone receptorENSG00000165409TSHRchr14:80954989-81146302:+                                                                                                                      0.11                                                                                                                                                  
delta like canonical Notch ligand 4ENSG00000128917DLL4chr15:40929340-40939072:+                                                                                                                                      0.11                                                                                                                                  
coagulation factor III, tissue factorENSG00000117525F3chr1:94529225-94541800:-                      0.11                                                                                                                                                                                                                                                  
adducin 3ENSG00000148700ADD3chr10:109996368-110135565:+              0.11                                                                                                                                                                                                                                                          
fibronectin leucine rich transmembrane protein 2ENSG00000185070FLRT2chr14:85530144-85654426:+                                                                                                                      0.1                                                                                                                                                  
cholinergic receptor nicotinic alpha 7 subunitENSG00000175344CHRNA7chr15:32030488-32172521:+                                                                                                                                              0.1                                                                                                                          
N-acylsphingosine amidohydrolase 2ENSG00000188611ASAH2chr10:50182778-50248610:-                                                              0.1                                                                                                                                                                                                          
cadherin 15ENSG00000129910CDH15chr16:89171767-89195492:+                                                                                                                                                                                                              0.1                                                          
scavenger receptor class B member 1ENSG00000073060SCARB1chr12:124776856-124882668:-                                                                                                                              0.1                                                                                                                                          
5'-nucleotidase ectoENSG00000135318NT5Echr6:85449584-85495791:+                      0.1                                                                                                                                                                                                                                                  
solute carrier family 16 member 3ENSG00000141526SLC16A3chr17:82228397-82261129:+                              0.1                                                                                                                                                                                                                                          

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