{"longTitle":"TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) segmented copy number","cohort":"TCGA lower grade glioma and glioblastoma (GBMLGG)","dataSubType":"copy number segments","security":"public","label":"Before remove germline cnv","tags":["cancer","nervous system"],"anatomical_origin":["Brian"],"name":"TCGA.GBMLGG.sampleMap/SNP6_genomicSegment","sample_type":["tumor"],"assembly":"hg19","type":"genomicSegment","version":"2017-09-08","unit":"log2(tumor/normal)","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) segmented copy number variation profile.<br><br> Copy number profile was measured experimentally using the Affymetrix Genome-Wide Human SNP Array 6.0 platform at the Broad TCGA genome characterization center. Raw copy numbers were estimated at each of the SNP and copy-number markers. <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/15475419\" target=\"_blank\"><u>Circular binary segmentation</u></a> was then used to segment the copy number data. Segments are mapped to hg19 genome assembly at Broad. Reference to the algorithm used by Broad to produce the dataset: <a href =\"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/lgg/cgcc/broad.mit.edu/genome_wide_snp_6/snp/broad.mit.edu_LGG.Genome_Wide_SNP_6.mage-tab.1.2020.0/DESCRIPTION.txt\" target=\"_blank\"> <u>DCC description</u></a> and <a href=\"http://www.nature.com/nature/journal/vaop/ncurrent/suppinfo/nature07385.html\" target=\"_blank\"><u>nature 2008</u></a> .<br><br>"}

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

TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) exon expression by RNAseq (polyA+ IlluminaHiSeq)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) PARADIGM inference activity (RNAseq)","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","tags":["cancer","nervous system"],"path":"data/public/TCGA/GBMLGG/Pathway_Paradigm_RNASeq","anatomical_origin":["Brian"],"name":"TCGA.GBMLGG.sampleMap/Pathway_Paradigm_RNASeq","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 on RNAseq data 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>"}