Hydroxymethylation analysis software tools | DNA methylation microarray data analysis
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are important epigenetic regulators of gene expression. 5mC and 5hmC levels can be computationally inferred at single base resolution using sequencing or array data from paired DNA samples that have undergone bisulfite and oxidative bisulfite conversion. Current estimation methods have been shown to produce irregular estimates of 5hmC level or are extremely computation intensive.
A method using maximum likelihood estimation to accurately estimate the parameters of unmethylated cytosine (5C), 5mC and 5hmC from Infinium microarray data given the signal intensities from the oxBS and BS replicates. The OxyBS tool can readily be applied to both the Illumina 450K and MethylationEPIC arrays as well as sequencing data with read counts for the four input data types (BS-methylated, BS-unmethylated, oxBSmethylated, and oxBS-unmethylated).
Provides a background correction method which uses a mixture of exponential and truncated normal distributions to flexibly model signal intensity and uses a truncated normal distribution to model background noise. Depending on data availability, three approaches are employed to estimate background normal distribution parameters using (i) internal chip negative controls, (ii) out-of-band Infinium I probe intensities or (iii) combined methylated and unmethylated intensities. Evaluation results in both duplicates and experimental standard samples showed that ENmix outperformed commonly used background subtraction methods in terms of improvement in replicability and accuracy as well as reducing probe design bias. After ENmix background correction the resulting data can be used with other commonly-used preprocessing methods including quantile normalization for between-sample normalization and BMIQ for further correction of probe-design bias.