{"name":"lat.vars.iCluster.redo.tumor","cohort":"TCGA Pan-Cancer (PANCAN)","type":"clinicalMatrix","version":"2017-08-21","url":"https://www.synapse.org/#!Synapse:syn10172423, https://www.synapse.org/#!Synapse:syn10380014","dataSubType":"iCluster","label":"iCluster latent variables"}

{"name":"StemnessScores_RNAexp_20170127.2.tsv","type":"clinicalMatrix","cohort":"TCGA Pan-Cancer (PANCAN)","dataSubType":"signatures","version":"2018-04-03","url":"https://www.synapse.org/#!Synapse:syn8079898, https://www.synapse.org/#!Synapse:syn8079918","label":"Stemness score (RNA based)","description":"The RNA based Stemness Scores derived by the Stemness group. <li><b>RNAss</b>: RNA expression-based (All set of available genes) this score will drive the main figures in PancanAtlas paper.</li> <li><b>EREG.EXPss</b>: Epigenetically regulated RNA expression-based (103 genes).</li>"}

{"name":"StemnessScores_DNAmeth_20170210.tsv","type":"clinicalMatrix","cohort":"TCGA Pan-Cancer (PANCAN)","dataSubType":"signatures","version":"2018-04-03","url":"https://www.synapse.org/#!Synapse:syn8079898, https://www.synapse.org/#!Synapse:syn8241793","label":"Stemness score (DNA methylation based)","description":"The DNA methylation based Stemness Scores derived by the Stemness group. <li><b>DNAss</b>: DNA methylation-based (Stem cell signature probes (219 probes), that combines the 3 signatures listed below). This score will drive the main figures in the PancanAtlas paper</li> <li><b>EREG-METHss</b>: Epigenetically regulated DNA methylation-based (87 probes).</li> <li><b>DMPss</b>: Differentially methylated probes-based (62 probes)</li> <li><b>ENHss</b>: Enhancer Elements/DNAmethylation-based (82 probes)</li>"}

{"name":"Subtype_Immune_Model_Based.txt","type":"clinicalMatrix","cohort":"TCGA Pan-Cancer (PANCAN)","dataSubType":"phenotype","version":"2018-04-03","label":"Immune subtype","description":"Model based immune subtype"}

{"name":"Survival_SupplementalTable_S1_20171025_xena_sp","cohort":"TCGA Pan-Cancer (PANCAN)","type":"clinicalMatrix","label":"Curated clinical data","description":"Curated clinical data from the Pan-cancer Atlas paper titled <a href=\"http://www.cell.com/cell/fulltext/S0092-8674(18)30229-0\">\"An Integrated TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR) to drive high quality survival outcome analytics\"</a>. The paper highlights four types of carefully curated survival endpoints, and <a href=\"http://www.cell.com/action/showFullTableImage?isHtml=true&tableId=tbl3&pii=S0092867418302290\"><B>recommends the use of the endpoints of OS, PFI, DFI, and DSS for each TCGA cancer type</B></a>.<br><br><li>OS: overall survial</li><li>PFI: progression-free interval</li><li>DSS: disease-specific survival</li><li>DFI: disease-free interval</li>","url":"http://www.cell.com/cell/fulltext/S0092-8674(18)30229-0","dataSubType":"phenotype","version":"2018-09-13","customcolor":{"description":{"url":"https://www.synapse.org/#!Synapse:syn8402823"},"cancer type abbreviation":{"HNSC":"#97D1A9","UVM":"#009444","GBM":"#B2509E","PAAD":"#6E7BA2","LUSC":"#A084BD","LAML":"#754C29","UCEC":"#FBE3C7","BRCA":"#ED2891","TGCT":"#BE1E2D","KICH":"#ED1C24","THCA":"#F9ED32","ACC":"#C1A72F","PCPG":"#E8C51D","LGG":"#D49DC7","COAD":"#9EDDF9","ESCA":"#007EB5","LUAD":"#D3C3E0","UCS":"#F89420","SARC":"#00A99D","OV":"#D97D25","LIHC":"#CACCDB","PRAD":"#7E1918","CHOL":"#104A7F","READ":"#DAF1FC","BLCA":"#FAD2D9","THYM":"#CEAC8F","MESO":"#542C88","KIRC":"#F8AFB3","KIRP":"#EA7075","SKCM":"#BBD642","DLBC":"#3953A4","CESC":"#F6B667","STAD":"#00AEEF"}}}