TCGA mesothelioma (MESO) copy number gistic2 thresholded estimate

{"owner":"TCGA","longTitle":"TCGA mesothelioma (MESO) reverse phase protein array","cohort":"TCGA Mesothelioma (MESO)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/meso/cgcc/mdanderson.org/mda_rppa_core/protein_exp/","dataSubType":"protein expression RPPA","security":"public","label":"RPPA","tags":["cancer"],"path":"data/public/TCGA/MESO/RPPA","anatomical_origin":["Lining of body cavities"],"name":"TCGA.MESO.sampleMap/RPPA","dataproducer":"MD Anderson Cancer Center TCGA proteome characterization center","wrangling_procedure":"Level_3 Data (file names: *.protein_expression.*) download from TCGA DCC, and processed at UCSC into Xena repository","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","type":"genomicMatrix","wrangler":"Xena TCGAscript RPPA processed on 2017-09-08","version":"2017-09-08","unit":"normalized RPPA value","primary_disease":"mesothelioma","platform":"M.D. Anderson Reverse Phase Protein Array Core platform","colnormalization":true,"description":"TCGA mesothelioma (MESO) protein expression by reverse phase protein array (RPPA).<br><br> The data was generated and processed at the MD Anderson Cancer Center TCGA proteome characterization center RPPA core. Level 3 interpreted level data was downloaded from TCGA data coordination center.<br><br>Data normalization from the MDACC RPPA core: <a href=\"http://bioinformatics.mdanderson.org/main/TCPA:Overview\" target=\"_blank\"><u>under section How are the RPPA data processed</u></a>.<br>"}

TCGA mesothelioma (MESO) reverse phase protein array

{"owner":"TCGA","longTitle":"TCGA mesothelioma (MESO) segmented copy number","cohort":"TCGA Mesothelioma (MESO)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/meso/cgcc/broad.mit.edu/genome_wide_snp_6/snp/","dataSubType":"copy number segments","security":"public","label":"Before remove germline cnv","tags":["cancer"],"path":"data/public/TCGA/MESO/SNP6_genomicSegment","anatomical_origin":["Lining of body cavities"],"name":"TCGA.MESO.sampleMap/SNP6_genomicSegment","dataproducer":"Broad Institute of MIT and Harvard University cancer genomic characterization center","wrangling_procedure":"Level_3 data download from TCGA DCC, processed at UCSC into cgData repository","sample_type":["tumor"],"assembly":"hg19","redistribution":true,"domain":"TCGA","type":"genomicSegment","wrangler":"cgData TCGAscript SNP6 processed on 2017-09-08","version":"2017-09-08","unit":"log2(tumor/normal)","primary_disease":"mesothelioma","platform":"SNP6","description":"TCGA mesothelioma (MESO) 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/meso/cgcc/broad.mit.edu/genome_wide_snp_6/snp/broad.mit.edu_MESO.Genome_Wide_SNP_6.mage-tab.1.2004.0/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>"}