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).

 

List 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 
T cell immunoglobulin and mucin domain containing 4ENSG00000145850TIMD4chr5:156919282-156963255:-                                                                                          1                                                                                                                                                                              
CD74 moleculeENSG00000019582CD74chr5:150401637-150412929:-                                                                                          1                                                                                                                    1                                                          
solute carrier family 17 member 9ENSG00000101194SLC17A9chr20:62952647-62969585:+                                                                                                                          1                                                                        1                                                                      
transmembrane protein 63BENSG00000137216TMEM63Bchr6:44126914-44155519:+                                          1                                                                                                                                                1                                                                              
diaphanous related formin 1ENSG00000131504DIAPH1chr5:141515016-141619055:-                                                                                          1                                                                                                                    1                                                          
protocadherin gamma subfamily C, 3ENSG00000240184PCDHGC3chr5:141475947-141512979:+                                                                                          1                                                                                                                    1                                                          
protocadherin gamma subfamily A, 9ENSG00000261934PCDHGA9chr5:141402932-141512979:+                                                                                          1                                                                                                                    1                                                          
protocadherin gamma subfamily A, 6ENSG00000253731PCDHGA6chr5:141373914-141512979:+                                                                                          1                                                                                                                    1                                                          
protocadherin gamma subfamily A, 10ENSG00000253846PCDHGA10chr5:141412987-141512979:+                                                                                          1                                                                                                                    1                                                          
protocadherin gamma subfamily A, 1ENSG00000204956PCDHGA1chr5:141330571-141512981:+                                                                                          1                                                                                                                    1                                                          
protocadherin gamma subfamily B, 7ENSG00000254122PCDHGB7chr5:141417645-141512979:+                                                                                          1                                                                                                                                                                              
solute carrier family 29 member 1 (Augustine blood group)ENSG00000112759SLC29A1chr6:44219505-44234151:+                                          1                                                                                                                                                1                                                                              
heat shock protein 90 alpha family class B member 1ENSG00000096384HSP90AB1chr6:44246166-44253888:+                                          1                                                                                                                                                1                                                                              
protocadherin beta 11ENSG00000197479PCDHB11chr5:141199582-141203779:+                                                                                          1                                                                                                                    1                                                          
protocadherin beta 12ENSG00000120328PCDHB12chr5:141208697-141212571:+                                                                                          1                                                                                                                    1                                                          
protocadherin beta 9ENSG00000177839PCDHB9chr5:141187127-141191541:+                                                                                          1                                                                                                                    1                                                          
protocadherin beta 10ENSG00000120324PCDHB10chr5:141187319-141195642:+                                                                                          1                                                                                                                    1                                                          
protocadherin beta 13ENSG00000187372PCDHB13chr5:141213919-141218979:+                                                                                          1                                                                                                                    1                                                          
protocadherin beta 14ENSG00000120327PCDHB14chr5:141222932-141227759:+                                                                                          1                                                                                                                    1                                                          
STEAP3 metalloreductaseENSG00000115107STEAP3chr2:119223831-119265652:+                                                          1                                                                                                                                                                                                              

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