{"longTitle":"TCGA kidney renal papillary cell carcinoma (KIRP) gene-level nonsilent somatic mutation (broad curated)","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_curated/mutations/","probeMap":"probeMap/hugo_gencode_good_hg19_V24lift37_probemap","dataSubType":"somatic non-silent mutation (gene-level)","security":"public","label":"broad curated","method":"MuTect","tags":["cancer"],"path":"data/public/TCGA/KIRP/mutation_curated_broad_gene","anatomical_origin":["Kidney"],"name":"TCGA.KIRP.sampleMap/mutation_curated_broad_gene","dataproducer":"Broad Institute Genome Sequencing Center","wrangling_procedure":"Download .maf file from TCGA DCC, processed into gene by sample matrix at UCSC, stored in the UCSC Xena repository","sample_type":["tumor"],"redistribution":true,"type":"genomicMatrix","wrangler":"xena TCGAscript maf processed on 2018-01-10","version":"2018-01-10","gdata_tags":["Broad Institute Genome Sequencing Center"],"unit":"binary non-silent mutation","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. <br><br> Red (=1) indicates that a non-silent somatic mutation (nonsense, missense, frame-shif indels, splice site mutations, stop codon readthroughs, change of start codon, inframe indels) was identified in the protein coding region of a gene, or any mutation identified in a non-coding gene. White (=0) indicates that none of the above mutation calls were made in this gene for the specific sample.<br><br>"}

TCGA kidney renal papillary cell carcinoma (KIRP) gene-level nonsilent somatic mutation (broad curated)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA kidney renal papillary cell carcinoma (KIRP) PARADIGM inference activity (array mRNA + CNV)","cohort":"TCGA Kidney Papillary Cell Carcinoma (KIRP)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/KIRP/20160128/","probeMap":"paradigmPathwayV1.probeMap","dataSubType":"PARADIGM pathway activity","security":"public","label":"expression (array) + CNV","tags":["cancer"],"path":"data/public/TCGA/KIRP/Pathway_Paradigm_mRNA_And_Copy_Number","anatomical_origin":["Kidney"],"name":"TCGA.KIRP.sampleMap/Pathway_Paradigm_mRNA_And_Copy_Number","dataproducer":"TCGA FIREHOSE pipeline","wrangling_procedure":"FIREHOSE data download from TCGA DCC, processed at UCSC into cgData repository","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","groupTitle":"TCGA kidney papillary cell carcinoma","type":"genomicMatrix","wrangler":"cgData TCGAscript Pathway_Paradigm processed on 2017-09-08","version":"2017-09-08","primary_disease":"kidney papillary cell carcinoma","description":"Broad FireHose automated run results of TCGA kidney renal papillary cell carcinoma (KIRP) gene activity level inferred using the PARADIGM method by integrating Agilent array mRNA data and copy number data.<br><br>PARADIGM (PMID 20529912) is pathway analysis method to infer tumor sample-specific genetic activities by incorporating curated pathway interactions as well as integrating diverse types of genomic data. The pathways used in this analysis are from <a href=\"http://pid.nci.nih.gov/\" target=\"_blank\"><u>NCI pathway interaction database</u></a>.<br><br>"}