A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways

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dc.contributor Aalto-yliopisto fi
dc.contributor Aalto University en
dc.contributor.author Äijö, Tarmo
dc.contributor.author Huang, Yun
dc.contributor.author Mannerström, Henrik
dc.contributor.author Chavez, Lukas
dc.contributor.author Tsagaratou, Ageliki
dc.contributor.author Rao, Anjana
dc.contributor.author Lähdesmäki, Harri
dc.date.accessioned 2017-05-11T08:35:57Z
dc.date.available 2017-05-11T08:35:57Z
dc.date.issued 2016-03-14
dc.identifier.citation Äijö , T , Huang , Y , Mannerström , H , Chavez , L , Tsagaratou , A , Rao , A & Lähdesmäki , H 2016 , ' A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways ' GENOME BIOLOGY , vol 17 , no. 1 , 49 , pp. 1-22 . DOI: 10.1186/s13059-016-0911-6 en
dc.identifier.issn 1474-7596
dc.identifier.other PURE UUID: 84ee4d92-3d3e-466e-b77f-fbf13a57bc42
dc.identifier.other PURE ITEMURL: https://research.aalto.fi/en/publications/a-probabilistic-generative-model-for-quantification-of-dna-modifications-enables-analysis-of-demethylation-pathways(84ee4d92-3d3e-466e-b77f-fbf13a57bc42).html
dc.identifier.other PURE LINK: http://www.scopus.com/inward/record.url?scp=84978805872&partnerID=8YFLogxK
dc.identifier.other PURE FILEURL: https://research.aalto.fi/files/11454387/art_10.1186_s13059_016_0911_6.pdf
dc.identifier.uri https://aaltodoc.aalto.fi/handle/123456789/25663
dc.description.abstract We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions. en
dc.format.extent 1-22
dc.format.mimetype application/pdf
dc.language.iso en en
dc.relation.ispartofseries GENOME BIOLOGY en
dc.relation.ispartofseries Volume 17, issue 1 en
dc.rights openAccess en
dc.subject.other Cell Biology en
dc.subject.other Ecology, Evolution, Behavior and Systematics en
dc.subject.other Genetics en
dc.subject.other 113 Computer and information sciences en
dc.title A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways en
dc.type A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä fi
dc.description.version Peer reviewed en
dc.contributor.department Tietojenkäsittelytieteen laito
dc.contributor.department Texas A and M University
dc.contributor.department Professorship Lähdesmäki H.
dc.contributor.department German Cancer Research Center
dc.contributor.department La Jolla Institute for Allergy and Immunology
dc.contributor.department Department of Computer Science
dc.subject.keyword 5-methylcytosine oxidation
dc.subject.keyword Bayesian analysis
dc.subject.keyword Bisulfite sequencing
dc.subject.keyword BS-seq/oxBS-seq/TAB-seq/fCAB-seq/CAB-seq/redBS-seq/MAB-seq
dc.subject.keyword DNA methylation
dc.subject.keyword Hierarchical modeling
dc.subject.keyword TET proteins
dc.subject.keyword Cell Biology
dc.subject.keyword Ecology, Evolution, Behavior and Systematics
dc.subject.keyword Genetics
dc.subject.keyword 113 Computer and information sciences
dc.identifier.urn URN:NBN:fi:aalto-201705114047
dc.identifier.doi 10.1186/s13059-016-0911-6
dc.type.version publishedVersion

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