MethCP: Differentially Methylated Region Detection with Change Point Models (bioRxiv)

1 MethCP: Differentially Methylated Region Detection with Change Point Models

Boying Gong, Elizabeth Purdom, MethCP: Differentially Methylated Region Detection with Change Point Models, 2018, bioRxiv.

https://doi.org/10.1101/265116

1.1 Summary

A new approach (MethCP) for the identification of differentially methylated regions (DMRS) of the DNA based on whole genome sequencing data is supposed. The approach is develope for more complex design than two-group comparisons, e.g. for time course experiments. For the two-group setup, it is claimed that MethCP outperforms existing approaches.

1.2 Study outcomes

1.2.1 Outcome O1

The performance of ...

Outcome O1 is presented as Figure X in the original publication.

1.2.2 Outcome O2

...

Outcome O2 is presented as Figure X in the original publication.

1.2.3 Outcome On

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Outcome On is presented as Figure X in the original publication.

1.2.4 Further outcomes

If intended, you can add further outcomes here.

1.3 Study design and evidence level

1.3.1 General aspects

You can describe general design aspects here. The study designs for describing specific outcomes are listed in the following subsections:

1.3.2 Design for Outcome O1

• The outcome was generated for ...
• Configuration parameters were chosen ...
• ...

1.3.3 Design for Outcome O2

• Publicly available data for Arabidopsis Thaliana [Coleman-Derr et al., 2012] with GEO accession number GSE39045 was analyzed
• Wildtype data was compared to H2Z.Z mutant
• The data had six replicates in both groups
• For assessing false-positives, the six control replicates were randomly assinged to two groups with three replicates AND by performing one of the two additional permutation approaches:

1. The two counts for methylated and unmethylated were permuted across samples for each CpG. This breaks local correlations within a sample but preserved correlations which occur over all/several samples. It also prohibits global differences between the samples in the average methylation level.
2. The CpG positions within a sample were permuted which breaks local correlations along the genome. This does not prevent potential global difference between the methylation levels of the individual samples.

1.5 References

Coleman-Derr, D. and Zilberman, D. 2012. Deposition of histone variant h2a. z within gene bodies regulates responsive genes. PLoS genetics 8, e1002988