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 
transmembrane serine protease 2ENSG00000184012TMPRSS2chr21:41464551-41531116:-                                                                                                                                                                                      0.41                                                                                  
cytochrome b-245 alpha chainENSG00000051523CYBAchr16:88643283-88651152:-                                                                                                                                      0.12                0.19                                                        0.1                                                          
CD52 moleculeENSG00000169442CD52chr1:26317957-26320523:+                                              0.18                                                                                                0.12                        0.1                                                                                                  
roundabout guidance receptor 3ENSG00000154134ROBO3chr11:124865386-124881470:+                                                                                                                                                              0.17                                        0.23                                                                  
G protein-coupled estrogen receptor 1ENSG00000164850GPER1chr7:1082208-1093815:+                                                                                                                                                              0.4                                                                                                          
protein tyrosine phosphatase receptor type GENSG00000144724PTPRGchr3:61561569-62297613:+                      0.17                                                        0.1                                                                                                                        0.13                                                                  
semaphorin 3GENSG00000010319SEMA3Gchr3:52433053-52445085:-                      0.17                                                                                                                                        0.23                                                                                                          
matrix remodeling associated 8ENSG00000162576MXRA8chr1:1352689-1361777:-                                                                                                                                              0.11                                                        0.28                                                                  
TNF receptor superfamily member 4ENSG00000186827TNFRSF4chr1:1211326-1214138:-                                                                                                                                              0.11                                                        0.28                                                                  
serine peptidase inhibitor, Kunitz type 1ENSG00000166145SPINT1chr15:40844018-40858207:+                              0.11                                                                                                        0.11                                                                        0.18                                                          
interferon gamma receptor 1ENSG00000027697IFNGR1chr6:137197484-137219449:-                                      0.1                                                                                                                0.14                                                        0.14                                                          
ecto-NOX disulfide-thiol exchanger 1ENSG00000120658ENOX1chr13:43213518-43786908:-                              0.23                                                                                                                        0.16                                                                                                                  
A-kinase anchoring protein 11ENSG00000023516AKAP11chr13:42272153-42323267:+                              0.22                                                                                                                        0.16                                                                                                                  
spectrin repeat containing nuclear envelope protein 2ENSG00000054654SYNE2chr14:63852983-64226433:+                                                                                                                      0.12                                        0.26                                                                                                          
FLVCR heme transporter 1ENSG00000162769FLVCR1chr1:212858255-212899363:+                                                                                                                                                              0.17                                        0.21                                                                  
EPH receptor A4ENSG00000116106EPHA4chr2:221418027-221574202:-                                                                              0.18                                                                0.19                                                                                                                          
transmembrane protein 30AENSG00000112697TMEM30Achr6:75252924-75284968:-                                      0.22                                                                                                                                                                0.16                                                                  
solute carrier family 12 member 6ENSG00000140199SLC12A6chr15:34229996-34338060:-                                                                                                                                                      0.37                                                                                                                  
peroxidasinENSG00000130508PXDNchr2:1631887-1744852:-                                                                                                                                                              0.18                                        0.19                                                                  
STAM binding protein like 1ENSG00000138134STAMBPL1chr10:88879734-88975153:+                                                      0.24        0.13                                                                                                                                                                                                          

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