TCGA brain lower grade glioma (LGG) gene expression (AgilentG4502A_07_3 array)

TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) DNA methylation (HumanMethylation450)

{"owner":"TCGA","longTitle":"TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) copy number gistic2 estimate","cohort":"TCGA lower grade glioma and glioblastoma (GBMLGG)","dataSubType":"copy number (gene-level)","security":"public","label":"gistic2","tags":["cancer","nervous system"],"path":"data/public/TCGA/GBMLGG/Gistic2_CopyNumber_Gistic2_all_data_by_genes","anatomical_origin":["Brian"],"name":"TCGA.GBMLGG.sampleMap/Gistic2_CopyNumber_Gistic2_all_data_by_genes","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","type":"genomicMatrix","version":"2017-09-08","unit":"Gistic2 copy number","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) 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, TCGA FIREHOSE pipeline applied GISTIC2 method to produce segmented CNV data, which was then mapped to genes to produce gene-level estimates. Genes are mapped onto the human genome coordinates using UCSC xena HUGO probeMap. Reference to GISTIC2 method PMID:21527027.<br><br>"}

TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) copy number gistic2 estimate

TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) gene expression by RNAseq (ployA+ IlluminaHiSeq), pancan normalized

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

{"longTitle":"TCGA brain lower grade glioma and glioblastoma multiforme (GBMLGG) segmented copy number (delete germline cnv)","cohort":"TCGA lower grade glioma and glioblastoma (GBMLGG)","dataSubType":"copy number segments","security":"public","label":"After remove germline cnv","tags":["cancer","nervous system"],"anatomical_origin":["Brian"],"name":"TCGA.GBMLGG.sampleMap/SNP6_nocnv_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 after removing common germline copy number variation.<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. A fixed set of common germline cnv probes were removed prior to segmentation. 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>"}