{"owner":"TCGA","longTitle":"TCGA pan-cancer PARADIGM IPL using RNAseq+CNV (Five3 Genomics)","cohort":"TCGA Pan-Cancer (PANCAN)","url":"https://www.synapse.org/#!Synapse:syn1695423","dataSubType":"PARADIGM pathway activity","security":"public","label":"Paradigm IPLs (Five3 Genomics)","tags":["PANCAN12","Esophagus","Lymphatic tissue","Brain","Pancreas","Testis","Lung","Rectum","Lining of body cavities","Paraganglia","Bladder","Kidney","Thyroid Gland","Stomach","Blood","Cervix","Uterus","Ovary","Soft tissue","Bone","White blood cell","Liver","Colon and Rectum","Head and Neck region","Prostate","Breast","Colon","Adrenal gland","Skin","non-small cell lung cancer","Gastric","cancer"],"path":"/inside/home/jzhu/cgDataJing/TCGAscripts/preFreezeCAVM/TCGA/PANCAN/merge_merged_reals","anatomical_origin":[""],"name":"TCGA.PANCAN.sampleMap/merge_merged_reals","dataproducer":"Five3 Genomics","wrangling_procedure":"Download from https://www.synapse.org/#!Synapse:syn1738372,deposited into UCSC Xena repository","sample_type":["tumor"],"redistribution":true,"domain":"TCGA","groupTitle":"TCGA  Pan-Cancer","type":"genomicMatrix","wrangler":"manually processed on 2013-09-12","version":"2013-09-12","primary_disease":"cancer","description":"Five3 Genomics PARADIGM pathway IPLs (integrated pathway levels) using RNAseq and copy number data. The RNAseq data is the platform-corrected PANCAN12 dataset from UNC. Genes were median-centered. The CNV data is SNP6 data from Broad Inst,removed germline cnvs.  The pathways used in this analysis are from a version of <a href=\"https://www.synapse.org/#!Synapse:syn2244294\" target=\"_blank\">the SuperPathway developed by Five3 Genomics</a>. Detail: https://www.synapse.org/#!Synapse:syn1695423.<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.<br><br>"}

TCGA pan-cancer PARADIGM IPL using RNAseq+CNV (Five3 Genomics)