TCGA lymphoid neoplasm diffuse large B-cell lymphoma (DLBC) PARADIGM inference activity (RNAseq)

{"cgdataversion":1,"owner":"TCGA","longTitle":"TCGA lymphoid neoplasm diffuse large B-cell lymphoma (DLBC) PARADIGM inference activity (RNAseq + CNV)","cohort":"TCGA Large B-cell Lymphoma (DLBC)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/DLBC/20160128/","probeMap":"paradigmPathwayV1.probeMap","dataSubType":"PARADIGM pathway activity","security":"public","label":"expression + CNV","tags":["cancer"],"path":"data/public/TCGA/DLBC/Pathway_Paradigm_RNASeq_And_Copy_Number","anatomical_origin":["Lymphatic tissue"],"name":"TCGA.DLBC.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 diffuse large B-cell lymphoma","type":"genomicMatrix","wrangler":"cgData TCGAscript Pathway_Paradigm processed on 2017-09-08","version":"2017-09-08","primary_disease":"diffuse large B-cell lymphoma","description":"Broad FireHose automated run results of TCGA lymphoid neoplasm diffuse large B-cell lymphoma (DLBC) 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 lymphoid neoplasm diffuse large B-cell lymphoma (DLBC) PARADIGM inference activity (RNAseq + CNV)

{"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":"HiSeq, 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","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."}