{"name":"MAF_Aug31_2016_sorted_A3A_A3B_comparePlus.sp","url":"https://www.synapse.org/#!Synapse:syn7511424,https://www.synapse.org/#!Synapse:syn7511422,https://www.synapse.org/#!Synapse:syn7437205","type":"clinicalMatrix","version":"2017-02-24","clinicalfeature":"clinicalFeature","cohort":"PCAWG (specimen centric)","dataSubType":"mutational signature","label":"APOBEC mutagenesis analysis","description":"<b>APOBECtCa_enrich</b>:\tThe fold enrichment of cytosine substitutions preceded by a 5' thymine and followed by a 3' adenine among all cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the contexts of tca.<br><b>BH_Fisher_p-value_tCa</b>:\tBenjamini-Hochberg-corrected p-value for statistical over-representation of APOBEC signature tCa mutations in a sample.<br><b>tCa_to_G+tCa_to_T</b>:\tThe total number of APOBEC signature tCa mutations in a sample, i.e. the number of cytosine to guanine substitutions in the sequence tca, cytosine to thymine substitutions in the sequence tca, guanine to cytosine substitutions in the sequence tga , and guanine to adenine substitutions in the sequence tga in the specified sample.<br><b>APOBEC_tCa_MutLoad_MinEstimate</b>:\tA minimum estimate of the number of APOBEC induced tCa mutations in a sample.  This estimate is calculated using the formula: [\"tCa_to_G+tCa_to_T\"]*[(\"APOBECtCa_enrich\"-1)/\"APOBECtCa_enrich\"] to determine the number of APOBEC signature tCa mutations in excess of what would be expected by random mutagenesis at tca or tga sequences.  Calculated values are rounded to the nearest whole number.  \"APOBEC_tCa_MutLoad_MinEstimate\" is calculated only for samples with a \"BH_Fisher_p-value_tCa\" =< 0.05, signifying a statistical over-representation of APOBEC tCa mutagenesis.  Samples with \"BH_Fisher_p-value_tCa\" > 0.05 receive a value of 0.<br><b>APOBECrtCa_enrich</b>:\tThe fold enrichment of cytosine substitutions preceded by a 5' purine thymine dinucleotide (i.e., at or gt) and followed by a 3' adenine among all cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the contexts of atca or gtca.<br><b>APOBECytCa_enrich</b>:\tThe fold enrichment of cytosine substitutions preceded by a 5' pyrimidine thymine dinucleotide (i.e., ct or tt) and followed by a 3' adenine among all cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the contexts of ctca or ttca.<br><b>APOBECytCa_enrich-APOBECrtCa_enrich</b>:\tThe difference obtained when \"APOBECrtCa_enrich\" is subtracted from \"APOBECytCa_enrich\".<br><b>rtCa_to_G+rtCa_to_T</b>:\tThe total number of APOBEC signature atCa or gtCa mutations in a sample, i.e. the number of cytosine to guanine substitutions in the sequences atca or gtca, cytosine to thymine substitutions in the sequences atca or gtca, guanine to cytosine substitutions in the sequences tgat or tgac, and guanine to adenine substitutions in the sequences tgat or tgac in the specified sample.<br><b>ytCa_to_G+ytCa_to_T</b>:\tThe total number of APOBEC signature ctCa or ttCa mutations in a sample, i.e. the number of cytosine to guanine substitutions in the sequences ctca or ttca, cytosine to thymine substitutions in the sequences ctca or ttca, guanine to cytosine substitutions in the sequences tgaa or tgag, and guanine to adenine substitutions in the sequences tgaa or tgag in the specified sample.<br><b>rtca+tgay</b>:\tThe number of times the sequences atca, gtca, tgat, and tgac occur in all the 41 nucleotide sequence contexts in a sample.<br><b>ytca+tgar</b>:\tThe number of times the sequences ctca, ttca, tgag, and tgaa occur in all the 41 nucleotide sequence contexts in a sample.<br><b>ntca+tgan</b>:\tThe sum of \"rtca+tgay\" and \"ytca+tgar\".<br><b>ytCa_rtCa_Fisher_p-value</b>:\tThe p-value for two-sided Fisher's exact test comparing the ratio of ytCa mutations to rtCa mutations vs. the ratio of unmutated ytca sequences to unmutated rtca sequences in all of the 41 nucleotide sequence contexts in a sample.  Thus, the first ratio is \"ytCa_to_G+ytCa_to_T\"/\"rtCa_to_G+rtCa_to_T\" while the second ratio is [\"ytca+tgar\" - (\"ytCa_to_G+ytCa_to_T\")]/[\"rtca+tgay\" - (\"rtCa_to_G+rtCa_to_T\")].<br><b>ytCa_rtCa_BH_Fisher_p-value</b>:\tBenjamini-Hochberg-corrected p-value for \"ytCa_rtCa_Fisher_p-value\", i.e., two-sided Fisher's exact test comparing the ratio of ytCa mutations to rtCa mutations vs. the ratio of unmutated ytca sequences to unmutated rtca sequences in all of the 41 nucleotide sequence contexts in a sample.  Computed using p.adjust() in R.<br><b>APOBEC_tCa_enrich_quartile</b>:\tQuartile of fold enrichment for APOBEC signature tCa mutations among samples with \"BH_Fisher_p-value_tCa\" =< 0.05 and \"ytCa_rtCa_BH_Fisher_p-value\" =< 0.05.  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.  Computed using type 1 of quantile() in R.<br><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>"}