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 
zinc and ring finger 3ENSG00000183579ZNRF3chr22:28883592-29057487:+      0.67                                                                                                                                                                                                                                                                  
plexin B1ENSG00000164050PLXNB1chr3:48403854-48430051:-                      0.16                                                                        0.18                                                                0.19                                        0.13                                                                  
microtubule associated protein 4ENSG00000047849MAP4chr3:47850690-48089272:-                      0.16                                                                        0.18                                                                0.2                                        0.13                                                                  
agrinENSG00000188157AGRNchr1:1020123-1056118:+                                                                                                                                              0.11        0.27                                                0.28                                                                  
solute carrier family 23 member 3ENSG00000213901SLC23A3chr2:219161465-219170095:-                              0.34                                0.13                                                                                0.19                                                                                                                          
PX domain containing serine/threonine kinase likeENSG00000168297PXKchr3:58332880-58426126:+                      0.17                0.17                                                                                                                        0.16                                        0.15                                                                  
cell adhesion molecule 1ENSG00000182985CADM1chr11:115169218-115504957:-              0.11        0.24        0.3                                                                                                                                                                                                                                          
layilinENSG00000204381LAYNchr11:111540280-111561745:+                      0.23                                                        0.17                                                                                                                        0.25                                                                  
fibronectin type III domain containing 10ENSG00000228594C1orf233chr1:1598012-1600096:-                              0.11                                                                                                                                                                        0.28                        0.12                                        0.14  
dopamine receptor D4ENSG00000069696DRD4chr11:637293-640706:+                                                              0.15                                                                                                0.5                                                                                                          
junctional adhesion molecule 3ENSG00000166086JAM3chr11:134068925-134152001:+                      0.22                                                                                                                        0.14                                                        0.29                                                                  
oligodendrocyte myelin glycoproteinENSG00000126861OMGchr17:31272013-31297539:-                                                                                                                                                              0.35                                        0.29                                                                  
ATPase Na+/K+ transporting subunit alpha 1ENSG00000163399ATP1A1chr1:116372668-116410261:+                                                              0.15                0.16                                                        0.14        0.19                                                                                                                          
myelin protein zero like 3ENSG00000160588MPZL3chr11:118226690-118252350:-              0.11        0.23        0.3                                                                                                                                                                                                                                          
delta like canonical Notch ligand 1ENSG00000198719DLL1chr6:170282206-170306565:-                                                                                                                                                              0.47                                                0.16                                                          
zinc finger FYVE-type containing 27ENSG00000155256ZFYVE27chr10:97737121-97760907:+                                      0.14                                                                                                                0.16        0.33                                                                                                          
synaptosome associated protein 23ENSG00000092531SNAP23chr15:42491233-42545356:+                                                                      0.11                                                                                0.34                                                        0.17                                                          
major facilitator superfamily domain containing 14AENSG00000156875HIAT1chr1:100038097-100083377:+                      0.11                                                                                                                0.12                0.39                                                                                                                  
transmembrane 9 superfamily member 3ENSG00000077147TM9SF3chr10:96518109-96587452:-                                      0.14                                                                                                                0.16        0.32                                                                                                          
calcium homeostasis modulator family member 2ENSG00000138172CALHM2chr10:103446786-103452402:-              0.1                                                                                                                                        0.2        0.32                                                                                                          

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