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 
RAB25, member RAS oncogene familyENSG00000132698RAB25chr1:156061160-156070514:+                                                                                                                                                                                          0.11                                                        0.33                      
S100 calcium binding protein A6ENSG00000197956S100A6chr1:153534599-153536244:-                                                                                                                                          0.27                                                0.17                                                                              
family with sequence similarity 174 member BENSG00000185442FAM174Bchr15:92617443-92809884:-                                                          0.23                                                                                                                                                0.2                                                              
solute carrier family 38 member 2ENSG00000134294SLC38A2chr12:46358189-46372867:-                                                                                                                                                                                                                                                          0.43              
tweety family member 3ENSG00000136295TTYH3chr7:2631951-2664802:+                                                                                                                                  0.11                            0.39                                            0.15        0.16                                                      
potassium two pore domain channel subfamily K member 1ENSG00000135750KCNK1chr1:233614004-233672512:+                  0.25                                                                                                        0.17                                                            0.1                                                                                  
CD59 molecule (CD59 blood group)ENSG00000085063CD59chr11:33698261-33736445:-          0.14                                                0.28                                                                                                                                                                                                              
dendrocyte expressed seven transmembrane proteinENSG00000164935DCSTAMPchr8:104339087-104356689:+                                                                                                                                                                                                                                                                  0.42      
NIPA like domain containing 2ENSG00000104361NIPAL2chr8:98189833-98294393:-                                                                                                                                                                                                                                                                  0.42      
regulating synaptic membrane exocytosis 2ENSG00000176406RIMS2chr8:103500748-104256094:+                                                                                                                                                                                                                                                                  0.42      
fibroblast growth factor receptor like 1ENSG00000127418FGFRL1chr4:1009936-1026897:+                                                                                                                                                          0.42                                                                                                              
solute carrier family 49 member 3ENSG00000169026MFSD7chr4:681829-689441:-                                                                                                                                                          0.42                                                                                                              
endoplasmic reticulum metallopeptidase 1ENSG00000099219ERMP1chr9:5765076-5833117:-          0.17                                                                0.25                                                                                    0.19                                                                                                0.12          
multiple C2 and transmembrane domain containing 2ENSG00000140563MCTP2chr15:94231538-94483952:+                          0.18                                0.24                                                                                                                                                                                                              
fibroblast growth factor receptor 1ENSG00000077782FGFR1chr8:38411138-38468834:-                                                                                                                                                                                                  0.26                                                0.15                      
oncostatin M receptorENSG00000145623OSMRchr5:38845858-38945596:+                                                                                                                                  0.22                                                                                0.19                                                      
receptor interacting serine/threonine kinase 1ENSG00000137275RIPK1chr6:3063991-3115187:+                                                              0.24                                                            0.18                                                                            0.14    0.23                                                              
synaptic vesicle glycoprotein 2AENSG00000159164SV2Achr1:149903318-149917882:-                                                                                                                                          0.28                                                                                0.12                                              
solute carrier family 4 member 11ENSG00000088836SLC4A11chr20:3227417-3239190:-                                                                                                                                                          0.3                                                                                        0.1                      
interleukin 1 receptor accessory proteinENSG00000196083IL1RAPchr3:190514051-190659750:+          0.16                                                                                                                                                                                                                0.23                                              

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