TCGA glioblastoma multiforme (GBM) gene expression (AgilentG4502A_07_2 array)

{"start_index":1,"owner":"TCGA","longTitle":"TCGA glioblastoma multiforme (GBM) somatic mutation (ucsc automated)","cohort":"TCGA Glioblastoma (GBM)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/gbm/gsc/ucsc.edu/illuminaga_dnaseq_automated/mutations/","dataSubType":"somatic mutation (SNPs and small INDELs)","security":"public","label":"ucsc automated","method":"RADIA","tags":["cancer","nervous system"],"path":"data/public/TCGA/GBM/mutation_ucsc_maf","anatomical_origin":["Brain"],"name":"TCGA.GBM.sampleMap/mutation_ucsc_maf","dataproducer":"University of Californis Santa Cruz GDAC","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":["University of Californis Santa Cruz GDAC"],"primary_disease":"glioblastoma multiforme","platform":"IlluminaGA","description":"TCGA glioblastoma multiforme (GBM) somatic mutation data. Sequencing data are generated on a IlluminaGA system. The calls are generated at University of Californis Santa Cruz GDAC using the RADIA method.","wholegenome":true}

TCGA glioblastoma multiforme (GBM) somatic mutation (ucsc automated)

{"owner":"TCGA","longTitle":"TCGA glioblastoma multiforme (GBM) gene-level non-silent somatic mutation (pancan awg)","cohort":"TCGA Glioblastoma (GBM)","url":"https://www.synapse.org/#!Synapse:syn1729383","dataSubType":"somatic non-silent mutation (gene-level)","security":"public","label":"PANCAN AWG","tags":["cancer","nervous system"],"path":"data/public/TCGA/GBM/mutation","anatomical_origin":["Brain"],"name":"TCGA.GBM.sampleMap/mutation","dataproducer":"TCGA PANCAN AWG","wrangling_procedure":"TCGA PANCAN strictly filtered maf files (file names: *_cleaned_filtered.maf) download from Synapse, processed into gene by sample matrix at UCSC into Xena repository","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","groupTitle":"TCGA glioblastoma multiforme","type":"genomicMatrix","wrangler":"Xena TCGAscript mutationMatrix processed on 2017-09-08","version":"2017-09-08","unit":"binary non-silent mutation","primary_disease":"glioblastoma multiforme","description":"TCGA glioblastoma multiforme (GBM) 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>"}