TCGA esophageal carcinoma (ESCA) gene-level nonsilent somatic mutation (ucsc automated)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA FFPE pilot phase II (FPPP) miRNA mature strand expression by RNAseq (IlluminaHiseq)","cohort":"TCGA Formalin Fixed Paraffin-Embedded Pilot Phase II (FPPP)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/fppp/cgcc/bcgsc.ca/illuminahiseq_mirnaseq/mirnaseq/","dataSubType":"miRNA mature strand expression RNAseq","security":"public","label":"IlluminaHiseq","tags":["cancer","formalin-fixed paraffin-embedded","FFPE"],"path":"data/public/TCGA/FPPP/miRNA_HiSeq_gene","anatomical_origin":[],"name":"TCGA.FPPP.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":"","platform":"IlluminaHiSeq_miRNASeq","colnormalization":true}

TCGA FFPE pilot phase II (FPPP) miRNA mature strand expression by RNAseq (IlluminaHiseq)

{"cohort":"TCGA Formalin Fixed Paraffin-Embedded Pilot Phase II (FPPP)","clinicalfeature":"TCGA.FPPP.sampleMap/FPPP_clinicalFeature","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/fppp/bcr/","label":"Phenotypes","version":"2016-04-27","dataSubType":"phenotype","type":"clinicalMatrix","name":"TCGA.FPPP.sampleMap/FPPP_clinicalMatrix"}

{"cohort":"TCGA Glioblastoma (GBM)","url":"http://rabit.dfci.harvard.edu/download/","dataSubType":"Transcription factor regulatory impact","citation":"Proc Natl Acad Sci U S A. 2015","label":"U133A, 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_GBM.U133A","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."}