TCGA rectum adenocarcinoma (READ) PARADIGM inference activity (array mRNA + CNV)

{"longTitle":"TCGA rectum adenocarcinoma (READ) copy number gistic2 thresholded estimate","cohort":"TCGA Rectal Cancer (READ)","min":-2,"url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/READ/20160128/","dataSubType":"copy number (gene-level)","security":"public","label":"gistic2 thresholded","max":2,"tags":["cancer"],"path":"data/public/TCGA/READ/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","anatomical_origin":["Rectum"],"name":"TCGA.READ.sampleMap/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","dataproducer":"TCGA FIREHOSE pipeline","wrangling_procedure":"FIREHOSE data download from TCGA DCC, processed at UCSC into xena repository","sample_type":["tumor"],"redistribution":true,"groupTitle":"TCGA rectum adenocarcinoma","type":"genomicMatrix","wrangler":"xena TCGAscript CopyNumber_Gistic2 processed on 2017-09-08","version":"2017-09-08","unit":"-2,-1,0,1,2: 2 copy del, 1 copy del, no change, amplification, high-amplification","primary_disease":"rectum adenocarcinoma","description":"TCGA rectum adenocarcinoma (READ) thresholded 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, GISTIC2 method was applied using the TCGA FIREHOSE pipeline to produce gene-level copy number estimates. GISTIC2 further thresholded the estimated values to -2,-1,0,1,2, representing homozygous deletion, single copy deletion, diploid normal copy, low-level copy number amplification, or high-level copy number amplification. Genes are mapped onto the human genome coordinates using UCSC xena HUGO probeMap. Reference to GISTIC2 method PMID:21527027.<br><br>"}

TCGA rectum adenocarcinoma (READ) copy number gistic2 thresholded estimate

{"owner":"TCGA","longTitle":"TCGA rectum adenocarcinoma (READ) reverse phase protein array","cohort":"TCGA Rectal Cancer (READ)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/read/cgcc/mdanderson.org/mda_rppa_core/protein_exp/","dataSubType":"protein expression RPPA","security":"public","label":"RPPA","tags":["cancer"],"path":"data/public/TCGA/READ/RPPA","anatomical_origin":["Rectum"],"name":"TCGA.READ.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":"rectum adenocarcinoma","platform":"M.D. Anderson Reverse Phase Protein Array Core platform","colnormalization":true,"description":"TCGA rectum adenocarcinoma (READ) 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>"}