TCGA head & neck squamous cell carcinoma (HNSC) PARADIGM inference activity (RNAseq + CNV)

{"cohort":"TCGA Head and Neck Cancer (HNSC)","clinicalfeature":"TCGA.HNSC.sampleMap/HNSC_clinicalFeature","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/hnsc/bcr/","label":"Phenotypes","version":"2016-04-27","dataSubType":"phenotype","type":"clinicalMatrix","name":"TCGA.HNSC.sampleMap/HNSC_clinicalMatrix"}

{"start_index":1,"owner":"TCGA","longTitle":"TCGA head & neck squamous cell carcinoma (HNSC) somatic mutation (broad curated)","cohort":"TCGA Head and Neck Cancer (HNSC)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/hnsc/gsc/broad.mit.edu/illuminaga_dnaseq_curated/mutations/","dataSubType":"somatic mutation (SNPs and small INDELs)","security":"public","label":"broad curated","method":"MuTect","tags":["cancer"],"path":"data/public/TCGA/HNSC/mutation_curated_broad","anatomical_origin":["Head and Neck region"],"name":"TCGA.HNSC.sampleMap/mutation_curated_broad","dataproducer":"Broad Institute Genome Sequencing Center","wrangling_procedure":"Download .maf file from TCGA DCC, removed any calls from WGS samples, processed into UCSC Xena mutation format, stored in the UCSC Xena repository","sample_type":["tumor"],"assembly":"hg19","redistribution":true,"domain":"TCGA","type":"mutationVector","wrangler":"TCGAscript maf processed on 2017-09-08","version":"2017-09-08","gdata_tags":["Broad Institute Genome Sequencing Center"],"primary_disease":"head & neck squamous cell carcinoma","platform":"IlluminaGA","description":"TCGA head & neck squamous cell carcinoma (HNSC) somatic mutation data. Sequencing data are generated on a IlluminaGA system. The calls are generated at Broad Institute Genome Sequencing Center using the MuTect method.","wholegenome":true}

TCGA head & neck squamous cell carcinoma (HNSC) somatic mutation (broad curated)

{"cohort":"TCGA Kidney Chromophobe (KICH)","url":"http://rabit.dfci.harvard.edu/download/","dataSubType":"Transcription factor regulatory impact","citation":"Proc Natl Acad Sci U S A. 2015","label":"HiSeqV2, by RABIT","author":"Peng Jiang, Matthew L. Freedman, Jun S. Liu, X. Shirley Liu","articletitle":"Inference of transcriptional regulation in cancers","name":"RABIT/separate_processed/RABIT_KICH.HiSeq.V2","dataproducer":"Peng Jiang, Matthew L. Freedman, Jun S. Liu, X. Shirley Liu","type":"clinicalMatrix","pmid":26056275,"description":"Regulatory impact of each Transcription Factor (TF) on tumor specific gene expression patterns calculated by the RABIT tool. The column names are TF names, and the row names are TCGA sample IDs. RABIT uses a linear model t-value (coefficient / stderr) to represent the TF regulatory impact to gene expression in each tumor, and show the t-value in each matrix cell. A positive t-value indicates the TF up-regulates its target genes and a negative value indicates the TF down-regulate its target genes."}