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 
par-3 family cell polarity regulatorENSG00000148498PARD3chr10:34109560-34815325:-                                                              1                1                                                                                                                                                                                          
small ArfGAP 1ENSG00000112305SMAP1chr6:70667776-70862015:+                                      1                                                                                                                                                                1                                                                  
scavenger receptor family member expressed on T cells 1ENSG00000214279SCART1chr10:133453928-133523558:+              1        1                                                                                                1                                                                                                                                                  
erythrocyte membrane protein band 4.1 like 2ENSG00000079819EPB41L2chr6:130839347-131063322:-                                                                      1                                                                                1                                                        1                                                          
chondroitin sulfate proteoglycan 5ENSG00000114646CSPG5chr3:47562239-47580792:-                      1                                                                                                                                        1                                                                                                          
ATPase copper transporting betaENSG00000123191ATP7Bchr13:51932673-52011494:-                              1                                        1                                                                                                                                                                                                  
actinin alpha 1ENSG00000072110ACTN1chr14:68874143-68979440:-                      1                                                                                                                                        1                                                                                                          
CD101 moleculeENSG00000134256CD101chr1:117001750-117036476:+                                                                              1                                                                1                                                                                                                          
macrophage stimulating 1 receptorENSG00000164078MST1Rchr3:49887002-49903873:-                      1                                                                        1                                                                                                                                                                          
G protein-coupled receptor 107ENSG00000148358GPR107chr9:130053426-130140169:+                                                                                                                                                              1                                                                                                1          
interleukin 17 receptor DENSG00000144730IL17RDchr3:57089982-57170306:-                      1                                                                                                                                        1                                                                                                          
solute carrier family 22 member 3ENSG00000146477SLC22A3chr6:160348268-160452581:+                                                                                                                                                      1                                                        1                                                          
EPH receptor B2ENSG00000133216EPHB2chr1:22710839-22921500:+                                                                                                                                              1                                                1                                                                          
C-X-C motif chemokine receptor 5ENSG00000160683CXCR5chr11:118883766-118897799:+              1                                                                                                                                                                                        1                                                                  
TNF receptor superfamily member 11aENSG00000141655TNFRSF11Achr18:62325287-62391292:+                                              1                                                                                                                                        1        1                                                                          
family with sequence similarity 171 member A2ENSG00000161682FAM171A2chr17:44353215-44363875:-                                                                                                                                                                                      1                                                                        1          
chloride intracellular channel 4ENSG00000169504CLIC4chr1:24745357-24844324:+                                                                                                                              1                1                                                                                                                          
melanocortin 1 receptorENSG00000258839MC1Rchr16:89912119-89920977:+                      1                                                                                                                1                                                                        1                                                          
solute carrier family 1 member 5ENSG00000105281SLC1A5chr19:46774883-46788594:-                                                                                                                                                              1                                                                                                          
glutamate ionotropic receptor NMDA type subunit 2DENSG00000105464GRIN2Dchr19:48394875-48444931:+                                                                                                                                                              1                                                                                                          

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