MEDME

MEDME models DNA methylation levels from MeDIP-microarray enrichment data to provide improved estimates of absolute and relative CpG methylation across the genome.

Key Features:

• Model-based analysis framework: Uses a model-based analysis framework to estimate methylation from MeDIP-microarray enrichment signals.
• Absolute and relative estimates: Predicts both absolute and relative DNA methylation levels genome-wide.
• Non-linear enrichment correction: Accounts for non-linear relationships between antibody enrichment in MeDIP/immunoprecipitation and true CpG methylation levels.
• Bisulfite validation: Correlates model-derived estimates with bisulfite genomic DNA sequencing measurements for validation.
• High-throughput applicability: Operates on MeDIP-microarray data in high-throughput experimental scenarios.
• Multi-scale interpretation: Provides outputs interpretable at single-locus and chromosome-wide scales.
• Comparative analysis: Supports comparative methylation analyses between samples, for example normal human melanocytes versus a melanoma cell strain.

Scientific Applications:

• Genome-wide methylation mapping: Estimating DNA methylation maps from MeDIP-microarray experiments.
• Calibration of antibody-based assays: Validating and calibrating MeDIP enrichment signals against bisulfite genomic DNA sequencing.
• Epigenetics and disease studies: Comparing methylation status between normal and disease samples (e.g., melanocytes versus melanoma) to investigate epigenetic alterations.
• Scale-dependent interpretation: Interpreting methylation changes at both single-locus and chromosome-wide levels to inform gene regulation analyses.

Methodology:

Performs model-based analysis of MeDIP-microarray enrichment to estimate absolute and relative DNA methylation levels and correlates model-derived estimates with bisulfite genomic DNA sequencing for validation.