qsea

QSEA is a comprehensive software tool that aims to simplify the computational analysis of MeDIP-seq data. Genome-wide enrichment of methylated DNA, followed by sequencing, is a popular technique that reasonably compromises experimental costs and genomic coverage. However, quantifying the enrichment signals in terms of absolute levels of methylation requires specific transformation, and the computational analysis of these experiments is complex.

QSEA includes a Bayesian statistical model that transforms the enrichment read counts to absolute methylation levels. This enhances interpretability and facilitates comparison with other methylation assays. The software tool also suggests several calibration strategies for the critical parameters of the model, either using additional data or fairly general assumptions. The calibration strategies help to improve the accuracy and precision of the results obtained from the analysis of MeDIP-seq data.

In addition, QSEA outperforms existing methods compared to bisulfite sequencing (BS) validation data. The software tool also generated a clinically relevant benchmark dataset consisting of methylation enrichment experiments (MeDIP-seq), BS-based validation experiments (Methyl-seq), as well as gene expression experiments (RNA-seq) derived from non-small cell lung cancer patients. The dataset analysis revealed that QSEA retrieves well-known lung tumor methylation markers causative for gene expression changes. This demonstrates the applicability of QSEA for clinical studies.

QSEA offers a comprehensive workflow for modeling and quantifying MeDIP-seq data.