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 
sphingosine-1-phosphate receptor 4ENSG00000125910S1PR4chr19:3172346-3180332:+                                                                                                                              0.14                                                                                                                                          
ras homolog family member BENSG00000143878RHOBchr2:20447074-20449445:+                                                                                                                                                              0.14                                                                                                          
adrenoceptor beta 2ENSG00000169252ADRB2chr5:148825245-148828687:+                                                                                                                                                                                                              0.14                                                          
protocadherin beta 4ENSG00000081818PCDHB4chr5:141121799-141125623:+                                                                                                                                                                                                              0.14                                                          
protocadherin beta 3ENSG00000113205PCDHB3chr5:141100473-141152636:+                                                                                                                                                                                                              0.14                                                          
protocadherin beta 5ENSG00000113209PCDHB5chr5:141135218-141138625:+                                                                                                                                                                                                              0.14                                                          
protocadherin beta 15ENSG00000113248PCDHB15chr5:141245349-141249365:+                                                                                                                                                                                                              0.14                                                          
myosin ICENSG00000197879MYO1Cchr17:1464098-1492812:-                                                                                                                              0.14                                                                                                                                          
scavenger receptor class F member 1ENSG00000074660SCARF1chr17:1633858-1645747:-                                                                                                                              0.14                                                                                                                                          
adhesion G protein-coupled receptor G6ENSG00000112414ADGRG6chr6:142301854-142446266:+                                                                                                                                                                                                              0.14                                                          
neuregulin 2ENSG00000158458NRG2chr5:139846779-140043299:-                                                                                                                                                                                                              0.14                                                          
leucine rich single-pass membrane protein 1ENSG00000181016LSMEM1chr7:112480853-112491062:+                                                                                                                                                                                                                                                              0.14          
protocadherin beta 2ENSG00000112852PCDHB2chr5:141094578-141098703:+                                                                                                                                                                                                              0.14                                                          
protocadherin alpha 7ENSG00000204963PCDHA7chr5:140834248-141012344:+                                                                                                                                                                                                              0.14                                                          
ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4ENSG00000113532ST8SIA4chr5:100806935-100903266:-                                                                                                                                                                                                                      0.14                                                  
transmembrane 4 L six family member 20ENSG00000168955TM4SF20chr2:227362156-227381995:-                                                              0.14                                                                                                                                                                                                          
heparin binding EGF like growth factorENSG00000113070HBEGFchr5:140332843-140346631:-                                                                                                                                                                                                              0.14                                                          
V-set domain containing T cell activation inhibitor 1ENSG00000134258VTCN1chr1:117143587-117210960:-                                                                                                                                      0.14                                                                                                                                  
claudin 23ENSG00000253958CLDN23chr8:8701938-8704106:+                                                                                                                              0.14                                                                                                                                          
immunoglobulin heavy constant alpha 1ENSG00000211895IGHA1chr14:105707118-105708665:-                                                                                                                              0.14                                                                                                                                          

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