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 
attractinENSG00000088812ATRNchr20:3471040-3651122:+                                                                                                                                                          0.29                                                                                        0.1                      
ATP binding cassette subfamily C member 5ENSG00000114770ABCC5chr3:183919934-184018015:-          0.17                                                                                                                                                                                                                0.22                                              
adaptor related protein complex 2 subunit mu 1ENSG00000161203AP2M1chr3:184174689-184184091:+          0.17                                                                                                                                                                                                                0.22                                              
abhydrolase domain containing 2, acylglycerol lipaseENSG00000140526ABHD2chr15:89087459-89202360:+                          0.19                                                                                                                                                                                0.2                                                              
chloride voltage-gated channel 2ENSG00000114859CLCN2chr3:184346185-184361651:-          0.17                                                                                                                                                                                            0.1                    0.22                                              
EPH receptor B3ENSG00000182580EPHB3chr3:184561784-184582409:+          0.17                                                                                                                                                                                                                0.22                                              
immunoglobulin superfamily member 8ENSG00000162729IGSF8chr1:160091340-160098943:-                                                          0.27                                                                                                                                0.11                                                                              
vomeronasal 1 receptor 1ENSG00000178201VN1R1chr19:57454790-57457142:-  0.21                0.17                                                                                                    0.18                                                                                                                                                  
G protein-coupled receptor 132ENSG00000183484GPR132chr14:105049389-105065445:-                                                                                                                                                          0.37                                                                                                              
immunoglobulin superfamily member 9ENSG00000085552IGSF9chr1:159927039-159945604:-                                                          0.27                                                                                                                                                                0.1                                              
transmembrane protein 117ENSG00000139173TMEM117chr12:43835967-44389762:+                                                                                                                                                                                                                                                          0.37              
leucine rich repeat and fibronectin type III domain containing 4ENSG00000173621LRFN4chr11:66856647-66860475:+                                                          0.26                                                                                                                        0.11                                                                                      
solute carrier organic anion transporter family member 5A1ENSG00000137571SLCO5A1chr8:69667047-69835064:-                                                                                                                                                                                                  0.14                                                                0.22      
insulin receptorENSG00000171105INSRchr19:7112255-7294034:-                                                                                                                                                                                                  0.36                                                                      
serine incorporator 3ENSG00000132824SERINC3chr20:44496221-44522109:-                                          0.22                                                                                                                                                0.14                                                                              
aspartate beta-hydroxylaseENSG00000198363ASPHchr8:61500556-61714640:-                                                                                                                                                                                                  0.15                                                                0.2      
fibroblast growth factor receptor 4ENSG00000160867FGFR4chr5:177086886-177098144:+                                                                                          0.34                                                                                                                                                                              
protein tyrosine phosphatase receptor type AENSG00000132670PTPRAchr20:2864184-3039076:+                                                                                                                                                          0.34                                                                                                              
lectin, mannose binding 2ENSG00000169223LMAN2chr5:177331562-177351852:-              0.11                                                                            0.34                                                                                                                                                                              
solute carrier family 34 member 1ENSG00000131183SLC34A1chr5:177379235-177398848:+                                                                                          0.34                                                                                                                                                                              

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