TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) segmented copy number (delete germline cnv)

{"owner":"TCGA","longTitle":"TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) gene-level non-silent somatic mutation (pancan awg)","cohort":"TCGA lower grade glioma and glioblastoma (GBMLGG)","dataSubType":"somatic non-silent mutation (gene-level)","security":"public","label":"PANCAN AWG","tags":["cancer","nervous system"],"path":"data/public/TCGA/GBMLGG/mutation","anatomical_origin":["Brian"],"name":"TCGA.GBMLGG.sampleMap/mutation","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","type":"genomicMatrix","version":"2017-09-08","unit":"binary non-silent mutation","primary_disease":"glioblastoma multiforme and brain lower grade glioma","description":"The dataset is combined from TCGA brain lower grade glioma and glioblastoma multiforme datasets. TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) somatic mutation data. Red (=1) indicates that a non-silent somatic mutation (nonsense, missense, frame-shif indels, splice site mutations, stop codon readthroughs) 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>Somatic mutations calls (even on the same tumor DNA extract) are affected by many factors including library prep, sequencing process, read mapping method, reference genome used, genome annotation, calling algorithms, and ad-hoc pre/postprocessing such as black list genes, target selection regions, and black list samples. This dataset is the best effort made by the TCGA PANCANCER Analysis Working Group. Raw PANCAN mutation data can be downloaded at the url site shown below.<br><br>"}

TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) gene-level non-silent somatic mutation (pancan awg)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) PARADIGM inference activity (array mRNA + CNV)","cohort":"TCGA lower grade glioma and glioblastoma (GBMLGG)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/GBMLGG/20160128/","probeMap":"paradigmPathwayV1.probeMap","dataSubType":"PARADIGM pathway activity","security":"public","label":"expression (array) + CNV","tags":["cancer","nervous system"],"path":"data/public/TCGA/GBMLGG/Pathway_Paradigm_mRNA_And_Copy_Number","anatomical_origin":["Brian"],"name":"TCGA.GBMLGG.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 glioblastoma multiforme and brain lower grade glioma","type":"genomicMatrix","wrangler":"cgData TCGAscript Pathway_Paradigm processed on 2017-09-08","version":"2017-09-08","primary_disease":"glioblastoma multiforme and brain lower grade glioma","description":"Broad FireHose automated run results of TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) 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>"}