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 
membrane magnesium transporter 1ENSG00000169446MMGT1chrX:135962070-135974063:-                                                                                                                                                                                                                  0.13                                                      
integrin subunit beta 1ENSG00000150093ITGB1chr10:32900319-33005792:-                                                                                                                                                                                                                  0.13                                                      
cholinergic receptor nicotinic beta 4 subunitENSG00000117971CHRNB4chr15:78624119-78727754:-                          0.13                                                                                                                                                                                                                                              
KIT proto-oncogene, receptor tyrosine kinaseENSG00000157404KITchr4:54657918-54740715:+                                                                                                                                                                                                          0.13                                                              
zinc finger DHHC-type palmitoyltransferase 5ENSG00000156599ZDHHC5chr11:57667747-57701187:+                                                          0.13                                                                                                                                                                                                    0.11          
major facilitator superfamily domain containing 6ENSG00000151690MFSD6chr2:190408355-190509205:+                          0.13                                                                                                                                                                                                                                              
endosome-lysosome associated apoptosis and autophagy regulator family member 2ENSG00000164659KIAA1324Lchr7:86876906-87059699:-                                                                                                                                                                                                                          0.13                                              
cysteine rich transmembrane BMP regulator 1ENSG00000150938CRIM1chr2:36355926-36551135:+                                                                                                                                                                                                                          0.13                                              
major facilitator superfamily domain containing 12ENSG00000161091MFSD12chr19:3538261-3574290:-                          0.13                                                                                                    0.14                                                                                                                        0.28        0.78          
adaptor related protein complex 2 subunit sigma 1ENSG00000042753AP2S1chr19:46838136-46850992:-  0.13                                                                                                                                                            0.33                                                                                                0.19          
solute carrier family 8 member A2ENSG00000118160SLC8A2chr19:47428017-47472168:-  0.13                                                                                                                                                                                                                                                                      
integrin subunit beta 8ENSG00000105855ITGB8chr7:20330702-20415754:+                                                                                                                                  0.13                                                                                                                                      
plexin A4ENSG00000221866PLXNA4chr7:132123332-132648688:-                                                                                                                  0.13                                                                                                                                                      
epithelial cell adhesion moleculeENSG00000119888EPCAMchr2:47345158-47387601:+                                                                                                                                                                                                                          0.13                                              
cholinergic receptor nicotinic alpha 5 subunitENSG00000169684CHRNA5chr15:78565520-78595269:+                          0.12                                                                                                                                                                                                                                              
syndecan 4ENSG00000124145SDC4chr20:45325288-45348424:-                                                                                                                                                                                          0.12                                                                              
pannexin 1ENSG00000110218PANX1chr11:94128928-94181972:+                                                          0.12                                                                                                                                                                                                    0.16          
integrin subunit alpha VENSG00000138448ITGAVchr2:186590065-186680901:+                          0.12                                                                                                                                                                                            0.16                                                  
neuregulin 4ENSG00000169752NRG4chr15:75935969-76059795:-                          0.12                                                                                                                                                                                                                                              
transmembrane protein 266ENSG00000169758C15orf27chr15:76059837-76229121:+                          0.12                                                                                                                                                                                                                                              

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