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 
protocadherin beta 6ENSG00000113211PCDHB6chr5:141150022-141153287:+                                                                                          0.29                                                                                                                    0.14                                                          
protocadherin beta 7ENSG00000113212PCDHB7chr5:141172619-141176383:+                                                                                          0.29                                                                                                                    0.14                                                          
protocadherin beta 8ENSG00000120322PCDHB8chr5:141177790-141180529:+                                                                                          0.29                                                                                                                    0.14                                                          
protocadherin beta 16ENSG00000272674PCDHB16chr5:141181399-141186399:+                                                                                          0.29                                                                                                                    0.14                                                          
catenin alpha 1ENSG00000044115CTNNA1chr5:138610967-138935034:+                                                                                          0.29                                                                                                                    0.13                                                          
solute carrier family 23 member 1ENSG00000170482SLC23A1chr5:139367196-139384553:-                                                                                          0.29                                                                                                                                                                              
syndecan 1ENSG00000115884SDC1chr2:20200797-20225433:-                          0.11                                                                                                                                    0.15                                                            0.18                                              
syndecan binding protein 2ENSG00000125775SDCBP2chr20:1309909-1329239:-                                                                                                                                                          0.29                                                                                                              
solute carrier family 7 member 4ENSG00000099960SLC7A4chr22:21028718-21032840:-                                                                                                                                                                                                                          0.29                                              
Bardet-Biedl syndrome 1ENSG00000174483BBS1chr11:66510606-66533627:+                                                          0.29                                                                                                                                                                                                              
fibroblast growth factor receptor 2ENSG00000066468FGFR2chr10:121478334-121598458:-                                                                                                                                                      0.19                                                            0.29                                                      
potassium calcium-activated channel subfamily M regulatory beta subunit 4ENSG00000135643KCNMB4chr12:70366276-70434292:+                                                                                                                                                                                                                          0.28                                              
neuropeptide Y receptor Y6 (pseudogene)ENSG00000226306NPY6Rchr5:137801193-137810751:+                                                                                          0.28                                                                                                                                                                              
low density lipoprotein receptor class A domain containing 3ENSG00000179241LDLRAD3chr11:35943981-36232136:+                          0.13                                                0.16                                                                                                                                                                                              
CDC42 small effector 2ENSG00000158985CDC42SE2chr5:131245493-131398447:+                                                                                          0.28                                                                                                                            0.11                                                  
solute carrier family 22 member 5ENSG00000197375SLC22A5chr5:132369752-132395614:+                                                                                          0.28                                                                                                                            0.1                                                  
solute carrier family 22 member 4ENSG00000197208SLC22A4chr5:132294443-132344206:+                                                                                          0.28                                                                                                                                                                              
ATP binding cassette subfamily A member 2ENSG00000107331ABCA2chr9:137007227-137028922:-                                                                                                                                                              0.22                                        0.17            0.17                                0.11            0.14          
thioredoxin domain containing 15ENSG00000113621TXNDC15chr5:134873803-134901525:+                                                                                          0.28                                                                                                                                                                              
solute carrier family 22 member 17ENSG00000092096SLC22A17chr14:23346306-23352912:-  0.28                                                                                                                                                                                                                                                                      

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