TCGA ovarian serous cystadenocarcinoma (OV) gene-level nonsilent somatic mutation (wustl)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA ovarian serous cystadenocarcinoma (OV) PARADIGM inference activity (array mRNA + CNV)","cohort":"TCGA Ovarian Cancer (OV)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/OV/20160128/","probeMap":"paradigmPathwayV1.probeMap","dataSubType":"PARADIGM pathway activity","security":"public","label":"expression (array) + CNV","tags":["cancer"],"path":"data/public/TCGA/OV/Pathway_Paradigm_mRNA_And_Copy_Number","anatomical_origin":["Ovary"],"name":"TCGA.OV.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 ovarian serous cystadenocarcinoma","type":"genomicMatrix","wrangler":"cgData TCGAscript Pathway_Paradigm processed on 2017-09-08","version":"2017-09-08","primary_disease":"ovarian serous cystadenocarcinoma","description":"Broad FireHose automated run results of TCGA ovarian serous cystadenocarcinoma (OV) 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 ovarian serous cystadenocarcinoma (OV) PARADIGM inference activity (array mRNA + CNV)

{"longTitle":"TCGA ovarian serous cystadenocarcinoma (OV) copy number gistic2 thresholded estimate","cohort":"TCGA Ovarian Cancer (OV)","min":-2,"url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/OV/20160128/","dataSubType":"copy number (gene-level)","security":"public","label":"gistic2 thresholded","max":2,"tags":["cancer"],"path":"data/public/TCGA/OV/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","anatomical_origin":["Ovary"],"name":"TCGA.OV.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 ovarian serous cystadenocarcinoma","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":"ovarian serous cystadenocarcinoma","description":"TCGA ovarian serous cystadenocarcinoma (OV) 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>"}