TCGA rectum adenocarcinoma (READ) gene-level nonsilent somatic mutation (bcm SOLiD)

TCGA rectum adenocarcinoma (READ) segmented copy number (delete germline cnv)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA rectum adenocarcinoma (READ) miRNA mature strand expression by RNAseq (IlluminaHiseq)","cohort":"TCGA Rectal Cancer (READ)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/read/cgcc/bcgsc.ca/illuminahiseq_mirnaseq/mirnaseq/","dataSubType":"miRNA mature strand expression RNAseq","security":"public","label":"IlluminaHiseq","tags":["cancer"],"path":"data/public/TCGA/READ/miRNA_HiSeq_gene","anatomical_origin":["Rectum"],"name":"TCGA.READ.sampleMap/miRNA_HiSeq_gene","dataproducer":"British Columbia Cancer Agency TCGA genome characterization center","wrangling_procedure":"Level_3 Data (file names: *.isoform.quantification.txt) download from TCGA DCC, for each sample, all isoform expression for the same miRNA mature strand are added together, log2(total_RPM +1) transformed, and deposited at UCSC into Xena repository.","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","type":"genomicMatrix","wrangler":"cgData TCGAscript miRNAseq processed on 2017-09-08","version":"2017-09-08","gdata_tags":["transcription","miRNA"],"unit":"log2(RPM+1)","primary_disease":"rectum adenocarcinoma","platform":"IlluminaHiSeq_miRNASeq","colnormalization":true}

TCGA rectum adenocarcinoma (READ) miRNA mature strand expression by RNAseq (IlluminaHiseq)

TCGA rectum adenocarcinoma (READ) exon expression by RNAseq (polyA+ IlluminaGA)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA rectum adenocarcinoma (READ) PARADIGM inference activity (array mRNA + CNV)","cohort":"TCGA Rectal Cancer (READ)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/READ/20160128/","probeMap":"paradigmPathwayV1.probeMap","dataSubType":"PARADIGM pathway activity","security":"public","label":"expression (array) + CNV","tags":["cancer"],"path":"data/public/TCGA/READ/Pathway_Paradigm_mRNA_And_Copy_Number","anatomical_origin":["Rectum"],"name":"TCGA.READ.sampleMap/Pathway_Paradigm_mRNA_And_Copy_Number","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 rectum adenocarcinoma","type":"genomicMatrix","wrangler":"cgData TCGAscript Pathway_Paradigm processed on 2017-09-08","version":"2017-09-08","primary_disease":"rectum adenocarcinoma","description":"Broad FireHose automated run results of TCGA rectum adenocarcinoma (READ) gene activity level inferred using the PARADIGM method by integrating Agilent array mRNA data and copy number data.<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>"}