TCGA lung adenocarcinoma (LUAD) PARADIGM inference activity (RNAseq + CNV)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA lung adenocarcinoma (LUAD) PARADIGM inference activity (array mRNA)","cohort":"TCGA Lung Adenocarcinoma (LUAD)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/LUAD/20160128/","probeMap":"paradigmPathwayV1.probeMap","dataSubType":"PARADIGM pathway activity","security":"public","label":"exprssion (array)","tags":["cancer","non-small cell lung cancer"],"path":"data/public/TCGA/LUAD/Pathway_Paradigm_mRNA","anatomical_origin":["Lung"],"name":"TCGA.LUAD.sampleMap/Pathway_Paradigm_mRNA","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 lung adenocarcinoma","type":"genomicMatrix","wrangler":"cgData TCGAscript Pathway_Paradigm processed on 2017-09-08","version":"2017-09-08","primary_disease":"lung adenocarcinoma","description":"Broad FireHose automated run results of TCGA lung adenocarcinoma (LUAD) gene activity level inferred using the PARADIGM method on gene expression data from Agilent array alone.<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 lung adenocarcinoma (LUAD) PARADIGM inference activity (array mRNA)

{"start_index":1,"owner":"TCGA","longTitle":"TCGA lung adenocarcinoma (LUAD) somatic mutation (broad curated)","cohort":"TCGA Lung Adenocarcinoma (LUAD)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/luad/gsc/broad.mit.edu/illuminaga_dnaseq_curated/mutations/","dataSubType":"somatic mutation (SNPs and small INDELs)","security":"public","label":"broad curated","method":"MuTect","tags":["cancer","non-small cell lung cancer"],"path":"data/public/TCGA/LUAD/mutation_curated_broad","anatomical_origin":["Lung"],"name":"TCGA.LUAD.sampleMap/mutation_curated_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":"lung adenocarcinoma","platform":"IlluminaGA","description":"TCGA lung adenocarcinoma (LUAD) 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.","wholegenome":true}