TCGA cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) PARADIGM inference activity (RNAseq)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) PARADIGM inference activity (RNAseq + CNV)","cohort":"TCGA Cervical Cancer (CESC)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/CESC/20160128/","probeMap":"paradigmPathwayV1.probeMap","dataSubType":"PARADIGM pathway activity","security":"public","label":"expression + CNV","tags":["cancer"],"path":"data/public/TCGA/CESC/Pathway_Paradigm_RNASeq_And_Copy_Number","anatomical_origin":["Cervix"],"name":"TCGA.CESC.sampleMap/Pathway_Paradigm_RNASeq_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 cervical & endocervical cancer","type":"genomicMatrix","wrangler":"cgData TCGAscript Pathway_Paradigm processed on 2017-09-08","version":"2017-09-08","primary_disease":"cervical & endocervical cancer","description":"Broad FireHose automated run results of TCGA cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) gene activity level inferred using the PARADIGM method by integrating RNAseq 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>"}

TCGA cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) PARADIGM inference activity (RNAseq + CNV)

{"longTitle":"TCGA cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) gene-level nonsilent somatic mutation (ucsc automated)","cohort":"TCGA Cervical Cancer (CESC)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/cesc/gsc/ucsc.edu/illuminaga_dnaseq_automated/mutations/","probeMap":"probeMap/hugo_gencode_good_hg19_V24lift37_probemap","dataSubType":"somatic non-silent mutation (gene-level)","security":"public","label":"ucsc automated","method":"RADIA","tags":["cancer"],"path":"data/public/TCGA/CESC/mutation_ucsc_maf_gene","anatomical_origin":["Cervix"],"name":"TCGA.CESC.sampleMap/mutation_ucsc_maf_gene","dataproducer":"University of Californis Santa Cruz GDAC","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":["University of Californis Santa Cruz GDAC"],"unit":"binary non-silent mutation","primary_disease":"cervical & endocervical cancer","platform":"IlluminaGA","description":"TCGA cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) somatic mutation data.  Sequencing data are generated on a IlluminaGA system. The calls are generated at University of Californis Santa Cruz GDAC using the RADIA 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>"}