{"cohort":"TCGA Breast Cancer (BRCA)","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_BRCA.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."}

TCGA breast invasive carcinoma (BRCA) DNA methylation (HumanMethylation27)

TCGA breast invasive carcinoma (BRCA) DNA methylation (HumanMethylation450)

{"longTitle":"TCGA breast invasive carcinoma (BRCA) copy number gistic2 estimate","cohort":"TCGA Breast Cancer (BRCA)","url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/BRCA/20160128/","dataSubType":"copy number (gene-level)","security":"public","label":"gistic2","tags":["cancer"],"path":"data/public/TCGA/BRCA/Gistic2_CopyNumber_Gistic2_all_data_by_genes","anatomical_origin":["Breast"],"name":"TCGA.BRCA.sampleMap/Gistic2_CopyNumber_Gistic2_all_data_by_genes","dataproducer":"TCGA FIREHOSE pipeline","wrangling_procedure":"FIREHOSE data download from TCGA DCC, processed at UCSC into xena repository","sample_type":["tumor"],"redistribution":true,"groupTitle":"TCGA breast invasive carcinoma","type":"genomicMatrix","wrangler":"xena TCGAscript CopyNumber_Gistic2 processed on 2017-09-08","version":"2017-09-08","unit":"Gistic2 copy number","primary_disease":"breast invasive carcinoma","description":"TCGA breast invasive carcinoma (BRCA) gene-level copy number variation (CNV) estimated using the GISTIC2 method.<br><br> Copy number profile was measured experimentally using whole genome microarray at a TCGA genome characterization center. Subsequently, TCGA FIREHOSE pipeline applied GISTIC2 method to produce segmented CNV data, which was then mapped to genes to produce gene-level estimates. Genes are mapped onto the human genome coordinates using UCSC xena HUGO probeMap. Reference to GISTIC2 method PMID:21527027.<br><br>"}