MADA

MADA performs comprehensive analysis of DNA methylation array data from Illumina Infinium methylation arrays to identify differential methylation and support downstream functional interpretation.

Key Features:

• Platform support: Processes data generated from Illumina Infinium methylation arrays.
• Pre-processing: Implements data loading, quality control, data filtering, and normalization of array data.
• Batch effect correction: Corrects technical variability across experimental batches to improve comparability.
• Differential methylation analysis: Identifies differentially methylated probes and regions between conditions or groups.
• Downstream functional analysis: Performs gene ontology and pathway enrichment analyses to interpret methylation changes.
• Cluster analysis: Performs clustering to explore sample groupings and methylation-based stratification.
• Visualization: Generates visualizations for pre-processing steps, differentially methylated probes or regions, and results from gene ontology, pathway, and cluster analyses.
• Workflow customization: Supports user-defined workflow configuration for tailored analysis sequences.

Scientific Applications:

• Differential methylation studies: Detects methylation differences between conditions, treatments, or phenotypic groups.
• Epigenetic mechanism investigation: Enables exploration of DNA methylation patterns associated with biological processes and complex diseases in the human genome.
• Functional interpretation: Links methylation alterations to biological functions and pathways via gene ontology and pathway enrichment.
• Sample stratification: Uses cluster analysis to identify methylation-defined subgroups within cohorts.
• Multi-batch study integration: Applies batch effect correction to combine data across experimental batches for comparative analyses.

Methodology:

Computational steps explicitly include data loading, quality control, data filtering, normalization, batch effect correction, differential methylation analysis to identify differentially methylated probes and regions, gene ontology and pathway enrichment analyses, cluster analysis, visualization of preprocessing and results, and configurable workflow specification.