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

ABSTRACT: To characterize the largely unknown functions of oxidised methylcytosines (oxi-mC; 5hmC/5fC/5caC) in DNA, several sequencing protocols have been recently developed. Quantitative analysis is complicated because DNA methylation modifications need to be deconvoluted from the data which is affected by several experimental parameters, including e.g. imperfect bisulphite conversion, oxidation efficiencies, various chemical labeling and protection steps, and sequencing errors. Here, we present a hierarchical generative model, Lux, for integrative analysis of any combination of BS-seq and “oxi-mC”-seq (BS-seq/oxBS-seq/TAB-seq/fCAB-seq/CAB-seq/redBS-seq/MAB-seq) data. We show that Lux improves quantification and comparison of methylation levels over existing methods and that Lux can easily proc

ORGANISM(S): Mus musculus

SUBMITTER: Tarmo Äijö 

PROVIDER: E-GEOD-68574 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress