{"cohort":"PCAWG (donor centric)","url":"https://www.synapse.org/#!Synapse:syn10333255, https://www.synapse.org/#!Synapse:syn10332949, https://www.synapse.org/#!Synapse:syn3354819","probeMap":"expressedPromoterCoordinates.probeMap","dataSubType":"alternative promoter activity","label":"relative promoter activity","name":"relativePromoterActivity.donor","wrangling_procedure":" Only tumor data are kept. When multiple tumor samples mapped a single donor, the average is taken and used for the donor. Promoter to gene mapping are based on : https://www.synapse.org/#!Synapse:syn10332989. Data are mapped to donor ids. 67989 promoters do not contribute to any transcription in any specimens. 45087 promoters contribute to transcription in at least one sample. All promoter data are kept in the matrix data file. Only the 45087 promoters with any activities are included in the promoter to gene mapping.","type":"genomicMatrix","version":"2017-09-26","unit":"portion of transcription activity of the gene driven by the promoter","description":"A gene has multiple promoters, each drives transcription of a different set of isoforms. The dataset describes their activity driving transcription. Promoter is defined as transcription start site. Values respresent relative promoter activity to each other, range from 0 to 1; and sum to 1 per gene per sample.  1 means 100% transcription activity of the gene is driven by the promoter. 0 means none of the transciption activity is driven from the promoter."}

{"name":"survival_donor","url":"https://www.synapse.org/#!Synapse:syn7772065, https://www.synapse.org/#!Synapse:syn4974831","version":"2017-02-25","cohort":"PCAWG (donor centric)","label":"overall survival","type":"clinicalMatrix","dataSubType":"phenotype"}

{"cohort":"PCAWG (donor centric)","url":"https://www.synapse.org/#!Synapse:syn5553991,https://www.synapse.org/#!Synapse:syn3104297,https://www.synapse.org/#!Synapse:syn2364711","probeMap":"gencode.v19.annotation.gene.probemap","dataSubType":"gene expression RNAseq","label":"normalized (fpkm-uq)","name":"tophat_star_fpkm_uq.v2_aliquot_gl.donor.log","wrangling_procedure":"RNAseq data are mapped from aliquote uuid to ICGC donor ids using http://pancancer.info/data_releases/may2016/pcawg_sample_sheet.v1.4.2016-09-14.tsv from https://wiki.oicr.on.ca/display/PANCANCER/Available+PCAWG+Data#AvailablePCAWGData-May2016Dataset,Version1.4 . Only tumor data are kept. When multiple tumors are available per donor, the avarage is used as the value for the donor.","type":"genomicMatrix","version":"2017-01-18","unit":"log2(fpkm-uq+0.001)","colnormalization":true,"description":"PCAWG-3 gene expression quantification (tumors only).<br><br>PCAWG-3 gene expression quantification (averaged from TopHat2 and STAR alignment derived gene expression estimations) in gene-level fpkm upper quartile normalized (FPKM-UQ) values, log2(x+0.001) transformed. This dataset only has gene expression from tumors, exlcluding all normal samples. FPKM-UQ has been shown to be a better normalization approach. The PCAWG-3 group recommends using FPKM-UQ values for gene expression quantification. Please see the PCAWG-3 wiki page for more information on normalization: https://wiki.oicr.on.ca/display/PANCANCER/Gene+expression+normalization.<br>"}