TCGA uterine corpus endometrioid carcinoma (UCEC) PARADIGM inference activity (RNAseq + CNV)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA uterine corpus endometrioid carcinoma (UCEC) PARADIGM inference activity (array mRNA)","cohort":"TCGA Endometrioid Cancer (UCEC)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/UCEC/20160128/","probeMap":"paradigmPathwayV1.probeMap","dataSubType":"PARADIGM pathway activity","security":"public","label":"exprssion (array)","tags":["cancer","uterus"],"path":"data/public/TCGA/UCEC/Pathway_Paradigm_mRNA","anatomical_origin":["Endometrium"],"name":"TCGA.UCEC.sampleMap/Pathway_Paradigm_mRNA","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 uterine corpus endometrioid carcinoma","type":"genomicMatrix","wrangler":"cgData TCGAscript Pathway_Paradigm processed on 2017-09-08","version":"2017-09-08","primary_disease":"uterine corpus endometrioid carcinoma","description":"Broad FireHose automated run results of TCGA uterine corpus endometrioid carcinoma (UCEC) gene activity level inferred using the PARADIGM method on gene expression data from Agilent array 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>"}

TCGA uterine corpus endometrioid carcinoma (UCEC) PARADIGM inference activity (array mRNA)

TCGA uterine corpus endometrioid carcinoma (UCEC) gene expression (AgilentG4502A_07_3 array)

{"longTitle":"TCGA esophageal carcinoma (ESCA) gene-level nonsilent somatic mutation (bcgsc automated)","cohort":"TCGA Esophageal Cancer (ESCA)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/esca/gsc/bcgsc.ca/illuminahiseq_dnaseq_automated/mutations/","probeMap":"probeMap/hugo_gencode_good_hg19_V24lift37_probemap","dataSubType":"somatic non-silent mutation (gene-level)","security":"public","label":"bcgsc automated","method":"BCGSC pipeline","tags":["cancer"],"path":"data/public/TCGA/ESCA/mutation_bcgsc_gene","anatomical_origin":["Esophagus"],"name":"TCGA.ESCA.sampleMap/mutation_bcgsc_gene","dataproducer":"Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC)","wrangling_procedure":"Download .maf file from TCGA DCC, processed into gene by sample matrix at UCSC, stored in the UCSC Xena repository","sample_type":["tumor"],"redistribution":true,"type":"genomicMatrix","wrangler":"xena TCGAscript maf processed on 2018-01-12","version":"2018-01-12","gdata_tags":["Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC)"],"unit":"binary non-silent mutation","primary_disease":"esophageal carcinoma","platform":"IlluminaHiSeq","description":"TCGA esophageal carcinoma (ESCA) somatic mutation data.  Sequencing data are generated on a IlluminaHiSeq system. The calls are generated at Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC) using the BCGSC pipeline method. <br><br> Red (=1) indicates that a non-silent somatic mutation (nonsense, missense, frame-shif indels, splice site mutations, stop codon readthroughs, change of start codon, inframe indels) was identified in the protein coding region of a gene, or any mutation identified in a non-coding gene. White (=0) indicates that none of the above mutation calls were made in this gene for the specific sample.<br><br>"}