TCGA thymoma (THYM) PARADIGM inference activity (RNAseq + CNV)

{"longTitle":"TCGA thymoma (THYM) gene-level nonsilent somatic mutation (ucsc automated)","cohort":"TCGA Thymoma (THYM)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thym/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/THYM/mutation_ucsc_maf_gene","anatomical_origin":["Thymus"],"name":"TCGA.THYM.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":"thymoma","platform":"IlluminaGA","description":"TCGA thymoma (THYM) 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>"}

TCGA thymoma (THYM) gene-level nonsilent somatic mutation (ucsc automated)

{"cohort":"TCGA Thyroid Cancer (THCA)","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_THCA.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."}