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 
voltage dependent anion channel 1ENSG00000213585VDAC1chr5:133971915-134005133:-                                                                                          0.28                                                                                                                                                                              
gonadotropin releasing hormone receptor 2 (pseudogene)ENSG00000211451GNRHR2chr1:145919013-145925341:+                                                                              0.16                                                        0.12    0.28                                                                                                                              
carbonic anhydrase 4ENSG00000167434CA4chr17:60149936-60170899:+          0.28                                                                                                                                                                                                                                                              
transmembrane protein 184AENSG00000164855TMEM184Achr7:1542235-1560821:-                                                                                                                                  0.11                            0.39                                                    0.16                                                      
tumor protein p53 inducible protein 13ENSG00000167543TP53I13chr17:29566052-29573157:+          0.26                                                                                                                                                                                                                                                              
GNAS complex locusENSG00000087460GNASchr20:58839718-58911192:+                                                                                                                                                                                                  0.26                                                                      
trans-golgi network protein 2ENSG00000152291TGOLN2chr2:85318020-85328425:-                                                                                                                                                                                                  0.26                                                                      
integrin subunit alpha 6ENSG00000091409ITGA6chr2:172427354-172506282:+                                                          0.26                                                                                                                                                                                                              
lemur tyrosine kinase 2ENSG00000164715LMTK2chr7:98106885-98209633:+                                                                                                                                                                  0.15                                                        0.11                                              
ArfGAP with dual PH domains 1ENSG00000105963ADAP1chr7:897901-955407:-                                                                                                                                  0.11                            0.4                                                    0.15                                                      
G protein-coupled receptor 137BENSG00000077585GPR137Bchr1:236142505-236221865:+                  0.26                                                                                                                                                                                                                                                      
protein kinase N1ENSG00000123143PKN1chr19:14433053-14471867:+  0.26                                                                                                                                                                                                                                                                      
ORAI calcium release-activated calcium modulator 3ENSG00000175938ORAI3chr16:30949066-30956461:+                                                                                                                                  0.11                                                                                                                0.14                      
transmembrane protein 150AENSG00000168890TMEM150Achr2:85598548-85603196:-                                                                                                                                                                                                  0.26                                                                      
gamma-glutamyl carboxylaseENSG00000115486GGCXchr2:85544723-85561547:-                                                                                                                                                                                                  0.26                                                                      
CLPTM1 regulator of GABA type A receptor forward traffickingENSG00000104853CLPTM1chr19:44954585-44993341:+  0.25                                                                                                                                                            0.3                                                                                                0.17          
TraB domain containing 2AENSG00000186854TRABD2Achr2:84821650-84907008:-                                                                                                                                                                                                  0.25                                                                      
CD83 moleculeENSG00000112149CD83chr6:14117256-14136918:+                                                                                                                                                                                                                                                                  0.25      
platelet derived growth factor receptor alphaENSG00000134853PDGFRAchr4:54229097-54298247:+                                                                                                                                                                                                  0.25                                                                      
pecanex 2ENSG00000135749PCNXL2chr1:232983435-233295713:-                  0.25                                                                                                                                                                                    0.24                                                                  

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