TCGA kidney renal clear cell carcinoma (KIRC) gene-level non-silent somatic mutation (pancan awg)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA kidney renal clear cell carcinoma (KIRC) PARADIGM inference activity (array mRNA + CNV)","cohort":"TCGA Kidney Clear Cell Carcinoma (KIRC)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/KIRC/20160128/","probeMap":"paradigmPathwayV1.probeMap","dataSubType":"PARADIGM pathway activity","security":"public","label":"expression (array) + CNV","tags":["cancer"],"path":"data/public/TCGA/KIRC/Pathway_Paradigm_mRNA_And_Copy_Number","anatomical_origin":["Kidney"],"name":"TCGA.KIRC.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 clear cell carcinoma","type":"genomicMatrix","wrangler":"cgData TCGAscript Pathway_Paradigm processed on 2017-09-08","version":"2017-09-08","primary_disease":"kidney clear cell carcinoma","description":"Broad FireHose automated run results of TCGA kidney renal clear cell carcinoma (KIRC) 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>"}

TCGA kidney renal clear cell carcinoma (KIRC) PARADIGM inference activity (array mRNA + CNV)

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