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).

 

List 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 
very low density lipoprotein receptorENSG00000147852VLDLRchr9:2621834-2660053:+                                                                                                                                                              1                                                                                                          
membrane associated ring-CH-type finger 1ENSG000001454161-Marchr4:163524298-164384050:-                                                                                                                                              1                                                                                                                          
dispatched RND transporter family member 2ENSG00000140323DISP2chr15:40358235-40378639:+                                                                                                                                                                                                              1                                                          
solute carrier family 6 member 20ENSG00000163817SLC6A20chr3:45755450-45796535:-                                                                                              1                                                                                                                                                                          
nucleoporin 210ENSG00000132182NUP210chr3:13316235-13420309:-                                                                                              1                                                                                                                                                                          
transient receptor potential cation channel subfamily M member 2ENSG00000142185TRPM2chr21:44350163-44443081:+                                                                                                                                                              1                                                                                                          
frizzled class receptor 2ENSG00000180340FZD2chr17:44557459-44559570:+                                                                                                                                                                                                                                                              1          
diacylglycerol lipase alphaENSG00000134780DAGLAchr11:61680433-61747001:+                                                                                                                                                                                                                                                              1          
phospholipase C delta 3ENSG00000161714PLCD3chr17:45108967-45133354:-                                                                                                                                                                                                                                                              1          
solute carrier family 38 member 3ENSG00000188338SLC38A3chr3:50205246-50221486:+                                                                                                                                                              1                                                                                                          
oxytocin receptorENSG00000180914OXTRchr3:8750408-8769628:-                                                                                              1                                                                                                                                                                          
G protein-coupled receptor 39ENSG00000183840GPR39chr2:132416574-132646559:+                                                                                                                                                                                      1                                                                                  
ribosomal protein SAENSG00000168028RPSAchr3:39406689-39412542:+                                                                                              1                                                                                                                                                                          
inducible T cell costimulator ligandENSG00000160223ICOSLGchr21:44222991-44240966:-                                                                                                                                                              1                                                                                                          
Ig-like domain-containing proteinENSG00000277117ICOSLGchr21:5022493-5040666:+                                                                                                                                                              1                                                                                                          
gap junction protein beta 6ENSG00000121742GJB6chr13:20221971-20232395:-                                                                              1                                                                                                                                                                                          
CUB domain containing protein 1ENSG00000163814CDCP1chr3:45082278-45146422:-                                                                                              1                                                                                                                                                                          
hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2ENSG00000099822HCN2chr19:589893-617159:+                                                              1                                                                                                                                                                                                          
leukocyte associated immunoglobulin like receptor 1ENSG00000167613LAIR1chr19:54351384-54370558:-                                                                                                                      1                                                                                                                                                  
tweety family member 1ENSG00000167614TTYH1chr19:54415219-54436900:+                                                                                                                      1                                                                                                                                                  

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