{"cohort":"PCAWG (donor centric)","url":"https://www.synapse.org/#!Synapse:syn8145655","probeMap":"JuncBASE_cassette.probeMap","dataSubType":"alternative splicing events","label":"JuncBASE - exon skipping (tumors only)","name":"JuncBASE_cassette.donor.xena","wrangling_procedure":"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":"2017-03-22","unit":"percent of exon inclusion","description":"cassette exon inclusion estimated by the JuncBASE method. 100 means 100% exon inclusion means (i.e. no exon skipping). 0 means 0% exon inclusion (i.e. the exon is completely skipped)."}

{"cohort":"PCAWG (donor centric)","url":"https://www.synapse.org/#!Synapse:syn8145655","probeMap":"JuncBASE_intron_retention.probeMap","dataSubType":"alternative splicing events","label":"JuncBASE - intron retention (tumors only)","name":"JuncBASE_intron_retention.donor.xena","wrangling_procedure":"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":"2017-03-22","unit":"percent of intron retention","description":"Intron retention inclusion estimated by the JuncBASE method. 100.0 means 100% retention."}

{"cohort":"PCAWG (donor centric)","url":"https://www.synapse.org/#!Synapse:syn7511424,https://www.synapse.org/#!Synapse:syn7511422,https://www.synapse.org/#!Synapse:syn7437205","dataSubType":"mutational signature","label":"APOBEC mutagenesis analysis","name":"MAF_Aug31_2016_sorted_A3A_A3B_comparePlus.donor","wrangling_procedure":"When multiple tumors are available per donor, classifications (if different) are concatenated for the donor.","clinicalfeature":"clinicalFeatureDonorAPOBEC","type":"clinicalMatrix","version":"2017-02-24","description":"<b>A3A_or_A3B</b>:\tAmong samples with a numerical value for \"APOBEC_tCa_enrich_quartile\", those samples with \"APOBECytCa_enrich-APOBECrtCa_enrich\" > 0 are denoted as \"A3A\" for A3A-like.  Conversely, those samples with \"APOBECytCa_enrich-APOBECrtCa_enrich\" < 0 are denoted as \"A3B\" for A3B-like.  Samples with \"BH_Fisher_p-value_tCa\" > 0.05 are denoted as \"NA\" for Not APOBEC-enriched.  Samples with \"BH_Fisher_p-value_tCa\" =< 0.05 but \"ytCa_rtCa_BH_Fisher_p-value\" > 0.05 are denoted as \"ND\" for Not Different from random mutagenesis at tca sequences.<br><br>More detailed parameter values are available in the corresponding specimen centric dataset.<br><br>"}