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 
consortin, connexin sorting proteinENSG00000162852CNSTchr1:246566444-246668584:+                  0.28                                                                                                        0.2                                                                            0.25    0.27                                        0.13                      
solute carrier family 52 member 2ENSG00000185803SLC52A2chr8:144354135-144361272:+                                                                                                                                                                                                  0.16        0.23                                                        0.48      
solute carrier family 39 member 4ENSG00000147804SLC39A4chr8:144409742-144416895:-                                                                                                                                                                                                  0.16        0.23                                                        0.48      
protein phosphatase 1 regulatory subunit 16AENSG00000160972PPP1R16Achr8:144477969-144502121:+                                                                                                                                                                                                  0.16        0.23                                                        0.48      
VPS28 subunit of ESCRT-IENSG00000160948VPS28chr8:144423601-144428563:-                                                                                                                                                                                                  0.16        0.23                                                        0.48      
LanC like 2ENSG00000132434LANCL2chr7:55365448-55433742:+                          0.15                                                                                                        0.23        0.49                                                                                                                              
transmembrane protein 8BENSG00000137103TMEM8Bchr9:35814451-35854847:+                                                                          0.3                                                                0.39                                                                        0.18                                                      
serine peptidase inhibitor, Kunitz type 2ENSG00000167642SPINT2chr19:38244035-38292614:+                          0.29                                                                                                                0.57                                                                                                                              
potassium two pore domain channel subfamily K member 6ENSG00000099337KCNK6chr19:38319844-38332076:+                          0.29                                                                                                                0.57                                                                                                                              
cytohesin 1ENSG00000108669CYTH1chr17:78674048-78782297:-          0.19                                                                                                                                0.2                                                        0.21        0.25                                                              
programmed cell death 1 ligand 2ENSG00000197646PDCD1LG2chr9:5510570-5571254:+          0.18                0.24                                                0.27                                                                                                                                        0.17                                                      
major facilitator superfamily domain containing 11ENSG00000092931MFSD11chr17:76735865-76781449:+          0.19                                                                                                                                0.22                                                        0.2        0.25                                                              
Rac family small GTPase 3ENSG00000169750RAC3chr17:82031624-82034204:+          0.21                                                    0.11                                                                                                                                    0.19        0.24                                                        0.2      
ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1ENSG00000186635ARAP1chr11:72685069-72793599:-                                                          0.84                                                                                                                                                                                                    0.1          
solute carrier family 20 member 2ENSG00000168575SLC20A2chr8:42416475-42541926:-                                          0.18                0.45                                                                        0.2                                                                                                                                      
solute carrier family 44 member 2ENSG00000129353SLC44A2chr19:10602457-10644559:+                                                                                                                                                                                                                                                          0.83              
major facilitator superfamily domain containing 2AENSG00000168389MFSD2Achr1:39955112-39969968:+          0.35                                                0.35                                                                        0.13                                                                                                                                      
cysteine rich hydrophobic domain 2ENSG00000109220CHIC2chr4:54009789-54064690:-                                                                                                                  0.22                                                                                0.25                        0.35                                              
solute carrier family 47 member 1ENSG00000142494SLC47A1chr17:19495385-19579034:+                                                                                                                          0.12                                                                        0.69                                                                      
CD44 molecule (Indian blood group)ENSG00000026508CD44chr11:35138870-35232402:+          0.15                0.15                                0.32                0.17                                                                                                                                                                                              

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