TCGA kidney renal papillary cell carcinoma (KIRP) gene-level nonsilent somatic mutation (bcm automated)

TCGA kidney renal papillary cell carcinoma (KIRP) DNA methylation (HumanMethylation450)

{"longTitle":"TCGA kidney renal papillary cell carcinoma (KIRP) copy number gistic2 estimate","cohort":"TCGA Kidney Papillary Cell Carcinoma (KIRP)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/KIRP/20160128/","dataSubType":"copy number (gene-level)","security":"public","label":"gistic2","tags":["cancer"],"path":"data/public/TCGA/KIRP/Gistic2_CopyNumber_Gistic2_all_data_by_genes","anatomical_origin":["Kidney"],"name":"TCGA.KIRP.sampleMap/Gistic2_CopyNumber_Gistic2_all_data_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 papillary cell carcinoma","type":"genomicMatrix","wrangler":"xena TCGAscript CopyNumber_Gistic2 processed on 2017-09-08","version":"2017-09-08","unit":"Gistic2 copy number","primary_disease":"kidney papillary cell carcinoma","description":"TCGA kidney renal papillary cell carcinoma (KIRP) 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, TCGA FIREHOSE pipeline applied GISTIC2 method to produce segmented CNV data, which was then mapped to genes to produce gene-level estimates. Genes are mapped onto the human genome coordinates using UCSC xena HUGO probeMap. Reference to GISTIC2 method PMID:21527027.<br><br>"}

TCGA kidney renal papillary cell carcinoma (KIRP) copy number gistic2 estimate

{"start_index":1,"owner":"TCGA","longTitle":"TCGA kidney renal papillary cell carcinoma (KIRP) somatic mutation (broad automated)","cohort":"TCGA Kidney Papillary Cell Carcinoma (KIRP)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/kirp/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/","dataSubType":"somatic mutation (SNPs and small INDELs)","security":"public","label":"broad automated","method":"MuTect","tags":["cancer"],"path":"data/public/TCGA/KIRP/mutation_broad","anatomical_origin":["Kidney"],"name":"TCGA.KIRP.sampleMap/mutation_broad","dataproducer":"Broad Institute Genome Sequencing Center","wrangling_procedure":"Download .maf file from TCGA DCC, removed any calls from WGS samples, processed into UCSC Xena mutation format, stored in the UCSC Xena repository","sample_type":["tumor"],"assembly":"hg19","redistribution":true,"domain":"TCGA","type":"mutationVector","wrangler":"TCGAscript maf processed on 2017-09-08","version":"2017-09-08","gdata_tags":["Broad Institute Genome Sequencing Center"],"primary_disease":"kidney papillary cell carcinoma","platform":"IlluminaGA","description":"TCGA kidney renal papillary cell carcinoma (KIRP) somatic mutation data. Sequencing data are generated on a IlluminaGA system. The calls are generated at Broad Institute Genome Sequencing Center using the MuTect method. When variant allele frequency information is available, only calls with VAF >4.0% are kept, resulting in 0 calls are kept and 0 calls are removed.","wholegenome":true}