seqlm

seqlm identifies differentially methylated regions (DMRs) in high-density DNA methylation data to enable regional analysis of methylation changes such as those measured by the Illumina 450K platform.

Key Features:

• DMR identification (MDL): Detects region boundaries using the minimum description length (MDL) principle to delineate contiguous differentially methylated regions.
• Statistical significance: Assesses significance of identified DMRs using linear mixed models.
• Performance and efficiency: Demonstrated higher sensitivity and specificity and faster runtime than compared methods on simulated and large publicly available methylation datasets, with minimal parameter tuning.
• Cross-platform validation: DMRs detected on sparse array data, such as Illumina 450K, have been confirmed using higher resolution sequencing approaches.

Scientific Applications:

• Gene regulation studies: Investigating the role of DNA methylation in gene regulation and expression.
• Disease epigenetics: Exploring epigenetic changes associated with diseases, including cancer and neurological disorders.
• Developmental epigenomics: Studying methylation pattern changes during development.

Methodology:

Detects DMR boundaries using the minimum description length (MDL) principle and evaluates region significance with linear mixed models; applied to high-density methylation data (e.g., Illumina 450K) and evaluated on simulated and large publicly available methylation datasets.