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 
interleukin 17 receptor AENSG00000177663IL17RAchr22:17084954-17115694:+                                                              1                                                                                                                                                                                                          
solute carrier family 12 member 2ENSG00000064651SLC12A2chr5:128083766-128189688:+                                                                                                                                                                                                                      1                                                  
microfibril associated protein 3ENSG00000037749MFAP3chr5:154038906-154220478:+                                                                                                                                                                                                              1                                                          
SLP adaptor and CSK interacting membrane proteinENSG00000161929SCIMPchr17:5208961-5234860:-                                                                                                                              1                                                                                                                                          
reticulon 4 receptor like 1ENSG00000185924RTN4RL1chr17:1934677-2025345:-                                                                                                                              1                                                                                                                                          
CXADR Ig-like cell adhesion moleculeENSG00000154639CXADRchr21:17512382-17593579:+                                                              1                                                                                                                                                                                                          
solute carrier family 9 member B2ENSG00000164038SLC9B2chr4:103019868-103085829:-                                                                                                                              1                                                                                                                                          
roundabout guidance receptor 1ENSG00000169855ROBO1chr3:78597240-79767815:-                                                                              1                                                                                                                                                                                          
C-X-C motif chemokine ligand 16ENSG00000161921CXCL16chr17:4733526-4739922:-                                                                                                                              1                                                                                                                                          
protocadherin 9ENSG00000184226PCDH9chr13:66302834-67230445:-                                                                      1                                                                                                                                                                                                  
leucyl and cystinyl aminopeptidaseENSG00000113441LNPEPchr5:96935394-97037515:+                                                                                                                                                                                                                      1                                                  
prolactin releasing hormone receptorENSG00000119973PRLHRchr10:118589989-118595699:-                                                                                                                      1                                                                                                                                                  
cystinosin, lysosomal cystine transporterENSG00000040531CTNSchr17:3636468-3661542:+                                                                                                                              1                                                                                                                                          
integrin subunit alpha EENSG00000083457ITGAEchr17:3714628-3801243:-                                                                                                                              1                                                                                                                                          
sphingolipid transporter 3 (putative)ENSG00000182557SPNS3chr17:4433688-4488208:+                                                                                                                              1                                                                                                                                          
transient receptor potential cation channel subfamily V member 1ENSG00000196689TRPV1chr17:3565444-3597098:-                                                                                                                              1                                                                                                                                          
adenosine A2b receptorENSG00000170425ADORA2Bchr17:15944917-15975746:+              1                                                                                                                                                                                                                                                          
monooxygenase DBH like 1ENSG00000079931MOXD1chr6:132296055-132401545:-                                                                                                                                                                                                              1                                                          
sphingomyelin synthase 2ENSG00000164023SGMS2chr4:107824563-107915047:+                                                                                                                              1                                                                                                                                          
teneurin transmembrane protein 2ENSG00000145934TENM2chr5:167284799-168264157:+              1                                                                                                                                                                                                                                                          

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