{"cohort":"TCGA Liver Cancer (LIHC)","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_LIHC.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."}

{"longTitle":"TCGA liver hepatocellular carcinoma (LIHC) gene-level nonsilent somatic mutation (bcgsc automated)","cohort":"TCGA Liver Cancer (LIHC)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/lihc/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/LIHC/mutation_bcgsc_gene","anatomical_origin":["Liver"],"name":"TCGA.LIHC.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":"liver hepatocellular carcinoma","platform":"IlluminaHiSeq","description":"TCGA liver hepatocellular carcinoma (LIHC) 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>"}