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 
angiopoietin 1ENSG00000154188ANGPT1chr8:107249482-107498055:-                                                                                                                                                                                                  1                                                                      
cyclin dependent kinase 16ENSG00000102225CDK16chrX:47217860-47229997:+                                                                                                                                                                                                                                                  1                      
desmoplakinENSG00000096696DSPchr6:7541575-7586717:+                                                                                                                          1                                                                                                                                              
frizzled class receptor 6ENSG00000164930FZD6chr8:103298433-103332866:+                                                                                                                                                                                                  1                                                                      
oxoglutarate receptor 1ENSG00000165621OXGR1chr13:96985719-96994730:-                  1                                                                                                                                                                                                                                                      
V-set and transmembrane domain containing 5ENSG00000214376VSTM5chr11:93818232-93850531:-                                                          1                                                                                                                                                                                                              
calreticulinENSG00000179218CALRchr19:12938578-12944489:+                          1                                                                                                                                                                                                                                              
family with sequence similarity 126 member AENSG00000122591FAM126Achr7:22889371-23014130:-                                                                                                                                  1                                                                                                                                      
potassium voltage-gated channel subfamily Q member 4ENSG00000117013KCNQ4chr1:40784012-40840452:+                                                                                                                                                                                                                                                  1                      
ADP ribosylation factor 1ENSG00000143761ARF1chr1:228082660-228099212:+                                                                                                                          1                                                                            1                                                                  
solute carrier family 36 member 4ENSG00000180773SLC36A4chr11:93144171-93197964:-                                                          1                                                                                                                                                                                                              
claudin 10ENSG00000134873CLDN10chr13:95433604-95579759:+                  1                                                                                                                                                                                                                                                      
microtubule actin crosslinking factor 1ENSG00000127603MACF1chr1:39081316-39487177:+                                                                                                                                  1                                                                                                                                      
ATPase phospholipid transporting 11CENSG00000101974ATP11CchrX:139726346-139945276:-                                                                                                                                                                                                                  1                                                      
claudin 12ENSG00000157224CLDN12chr7:90383721-90513402:+                                                                                                                                                                                                                          1                                              
STEAP family member 1ENSG00000164647STEAP1chr7:90154375-90164829:+                                                                                                                                                                                                                          1                                              
protein tyrosine kinase 6ENSG00000101213PTK6chr20:63528001-63537370:-                                                                                                                                                                                          1                                                                              
membrane palmitoylated protein 1ENSG00000130830MPP1chrX:154778684-154821007:-                                                                                                                          1                                                                                                                                              
cell adhesion associated, oncogene regulatedENSG00000064309CDONchr11:125955796-126063335:-              1                1                            1                                                                                                    1                                                                                                          
solute carrier family 9 member A6ENSG00000198689SLC9A6chrX:135985424-136047269:+                                                                                                                                                                                                                  1                                                      

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