{"longTitle":"TCGA pan-cancer gene-level copy number (gistic2_thresholded)","cohort":"TCGA Pan-Cancer (PANCAN)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/","dataSubType":"copy number (gene-level)","security":"public","label":"gene-level copy number (gistic2_thresholded)","tags":["cancer","non-small cell lung cancer","gastric cancer","pancancer","Adrenal gland","Esophagus","Rectum","Endometrium","Brian","Head and Neck region","Thymus","Lung","Blood","Soft tissue","Bone","Stomach","Colon and Rectum","Prostate","Breast","Ovary","Kidney","Lymphatic tissue","Brain","Thyroid Gland","Bladder","Paraganglia","Cervix","Uterus","Liver","Bile duct","Eye","Skin","Colon","Testis","Lining of body cavities","White blood cell","Pancreas"],"path":"/inside/home/jzhu/cgDataJing/TCGAscripts/preFreezeCAVM/TCGA/PANCAN/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","anatomical_origin":"","name":"TCGA.PANCAN.sampleMap/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","dataproducer":"UCSC Xena team","wrangling_procedure":"Data is combined from all TCGA cohorts and deposited into UCSC Xena repository","sample_type":["tumor"],"redistribution":true,"type":"genomicMatrix","version":"2016-08-16","unit":"-2,-1,0,1,2: 2 copy del,1 copy del,no change,amplification,high-amplification","primary_disease":"cancer","description":"TCGA pan-cancer gene-level copy number variation (CNV) estimated using the GISTIC2 threshold method,compiled using data from all TCGA cohorts. Copy number was measured experimentally using whole genome microarray at a TCGA genome characterization center. Subsequently,GISTIC2 method was applied using the TCGA FIREHOSE pipeline to produce gene-level copy number estimates. GISTIC2 further thresholded the estimated values to -2,-1,0,1,2,representing homozygous deletion,single copy deletion,diploid normal copy,low-level copy number amplification,or high-level copy number amplification. Genes are mapped onto the human genome coordinates using UCSC cgData HUGO probeMap. Reference to GISTIC2 method PMID:21527027.<br><br>"}