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 
exocyst complex component 7ENSG00000182473EXOC7chr17:76081017-76121576:-          0.21                                                                                                                                0.25                                                        0.24        0.25                                                        0.14      
talin 1ENSG00000137076TLN1chr9:35696948-35732395:-                                                                          0.31                                                                0.39                        0.19                                                0.18                                            0.13          
transmembrane protein 104ENSG00000109066TMEM104chr17:74776483-74839779:+          0.21                                                                                                                                0.23                                                        0.24        0.24                                                        0.14      
p21 (RAC1) activated kinase 1ENSG00000149269PAK1chr11:77321707-77474635:-                  0.62                                        0.28                                                                                                                                                                                        0.16            0.15          
natriuretic peptide receptor 2ENSG00000159899NPR2chr9:35792154-35809732:+                                                                          0.29                                                                0.39                        0.19                                                0.18                                                      
solute carrier family 6 member 13ENSG00000010379SLC6A13chr12:220621-262873:-                                                                                                                                                          0.47                                                                0.57                                              
calcium activated nucleotidase 1ENSG00000171302CANT1chr17:78991717-79009867:-          0.19                                                                                                                                0.21                                                        0.21        0.25                                                        0.17      
ELKS/RAB6-interacting/CAST family member 1ENSG00000082805ERC1chr12:990509-1495933:+                  0.18                                                                                                                        0.22                0.46        0.14                                                                                                      
tetraspanin 9ENSG00000011105TSPAN9chr12:3077355-3286564:+                                          0.16                                                                                                0.21                                                                                0.57                                              
TUB like protein 3ENSG00000078246TULP3chr12:2877223-2941140:+                                          0.15                                                                                                0.21                0.47        0.12                                                                                                      
lymphocyte antigen 6 family member EENSG00000160932LY6Echr8:143017982-143023832:+                                                                                                                                                                                                  0.19        0.24                                                        0.5      
DC-STAMP domain containing 2ENSG00000163354DCST2chr1:155018520-155033781:-                          0.19        0.53                        0.21                                                                                                                                                                                                              
unc-93 homolog B1, TLR signaling regulatorENSG00000110057UNC93B1chr11:67991104-68004982:-                                                          0.64                                                                                                                        0.1                                                                0.19                      
scribble planar cell polarity proteinENSG00000180900SCRIBchr8:143790920-143815379:-                                                                                                                                                                                                  0.19        0.24                                                        0.5      
neutral cholesterol ester hydrolase 1ENSG00000144959NCEH1chr3:172630249-172711218:-          0.18                0.74                                                                                                                                                                                                                                              
late endosomal/lysosomal adaptor, MAPK and MTOR activator 1ENSG00000149357LAMTOR1chr11:72085895-72103387:-                                                          0.92                                                                                                                                                                                                    0.1          
B cell receptor associated protein 31ENSG00000185825BCAP31chrX:153700497-153724697:-                          0.22                                0.26                0.14                                                0.12                                                                                        0.17                                                      
protein tyrosine kinase 2ENSG00000169398PTK2chr8:140657900-141002216:-                                                                                                                                                                                                  0.19        0.23                                                        0.5      
mal, T cell differentiation protein 2 (gene/pseudogene)ENSG00000147676MAL2chr8:119165034-119245673:+                                                                                                                          0.38                                                                                                                                        0.53      
CD274 moleculeENSG00000120217CD274chr9:5450503-5470566:+          0.18                0.29                                                0.28                                                                                    0.19                                                    0.16                                                      

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