TCGA acute myeloid leukemia (LAML) gene-level nonsilent somatic mutation (wustl)

{"longTitle":"TCGA acute myeloid leukemia (LAML) copy number gistic2 thresholded estimate","cohort":"TCGA Acute Myeloid Leukemia (LAML)","min":-2,"url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/LAML/20160128/","dataSubType":"copy number (gene-level)","security":"public","label":"gistic2 thresholded","max":2,"tags":["cancer"],"path":"data/public/TCGA/LAML/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","anatomical_origin":["White blood cell"],"name":"TCGA.LAML.sampleMap/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","dataproducer":"TCGA FIREHOSE pipeline","wrangling_procedure":"FIREHOSE data download from TCGA DCC, processed at UCSC into xena repository","sample_type":["tumor"],"redistribution":true,"groupTitle":"TCGA acute myeloid leukemia","type":"genomicMatrix","wrangler":"xena TCGAscript CopyNumber_Gistic2 processed on 2017-09-08","version":"2017-09-08","unit":"-2,-1,0,1,2: 2 copy del, 1 copy del, no change, amplification, high-amplification","primary_disease":"acute myeloid leukemia","description":"TCGA acute myeloid leukemia (LAML) thresholded gene-level copy number variation (CNV) estimated using the GISTIC2 method.<br><br> Copy number profile 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 xena HUGO probeMap. Reference to GISTIC2 method PMID:21527027.<br><br>"}

TCGA acute myeloid leukemia (LAML) copy number gistic2 thresholded estimate

TCGA acute myeloid leukemia (LAML) segmented copy number

{"name":"unc_v2_exon_hg19_probe_TCGA","assembly":"hg19","dbxref":"TCGA unc RNAseqV2 exon.quantification.txt","type":"probeMap","version":"2018-07-26","url":"https://portal.gdc.cancer.gov/legacy-archive/files/05c2e882-3cdb-4392-9d2f-916ef72bef7b","notes":"missing some exons due to the exon results we got also missed those exons","idtype":"exon","label":"exon annotation TCGA GAF version, UNC v2 analysis pipeline (hg19)"}