TCGA kidney chromophobe (KICH) gene-level nonsilent somatic mutation (broad)

TCGA kidney chromophobe (KICH) segmented copy number (delete germline cnv)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA kidney chromophobe (KICH) miRNA mature strand expression by RNAseq (IlluminaHiseq)","cohort":"TCGA Kidney Chromophobe (KICH)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/kich/cgcc/bcgsc.ca/illuminahiseq_mirnaseq/mirnaseq/","dataSubType":"miRNA mature strand expression RNAseq","security":"public","label":"IlluminaHiseq","tags":["cancer"],"path":"data/public/TCGA/KICH/miRNA_HiSeq_gene","anatomical_origin":["Kidney"],"name":"TCGA.KICH.sampleMap/miRNA_HiSeq_gene","dataproducer":"British Columbia Cancer Agency TCGA genome characterization center","wrangling_procedure":"Level_3 Data (file names: *.isoform.quantification.txt) download from TCGA DCC, for each sample, all isoform expression for the same miRNA mature strand are added together, log2(total_RPM +1) transformed, and deposited at UCSC into Xena repository.","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","type":"genomicMatrix","wrangler":"cgData TCGAscript miRNAseq processed on 2017-09-08","version":"2017-09-08","gdata_tags":["transcription","miRNA"],"unit":"log2(RPM+1)","primary_disease":"kidney chromophobe","platform":"IlluminaHiSeq_miRNASeq","colnormalization":true}

TCGA kidney chromophobe (KICH) miRNA mature strand expression by RNAseq (IlluminaHiseq)

{"longTitle":"TCGA kidney chromophobe (KICH) copy number gistic2 thresholded estimate","cohort":"TCGA Kidney Chromophobe (KICH)","min":-2,"url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/KICH/20160128/","dataSubType":"copy number (gene-level)","security":"public","label":"gistic2 thresholded","max":2,"tags":["cancer"],"path":"data/public/TCGA/KICH/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","anatomical_origin":["Kidney"],"name":"TCGA.KICH.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 kidney chromophobe","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":"kidney chromophobe","description":"TCGA kidney chromophobe (KICH) 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>"}