epidecodeR

epidecodeR analyzes the impact of epigenetic and epitranscriptomic modifications on gene dysregulation by integrating modification data types and dysregulated gene lists to identify relationships between modification degrees and gene expression shifts.

Key Features:

• Multi-modality integration: Integrates various modification data types with dysregulated gene lists.
• Cumulative distribution function analysis: Evaluates statistical significance in differential expression of genes grouped by the number of 'epi-marks'.
• Epigenetic modification analysis: Predicts roles of histone modifications including H3K9ac and H3K27ac in associated gene expression.
• Epitranscriptomic modification analysis: Analyzes N6-methyl-adenosine (m6A)-associated gene expression.

Scientific Applications:

• Deacetylase knockdown studies: Predicts roles of H3K9ac and H3K27ac in gene expression after knocking down deacetylases FAM60A and SDS3.
• Reader protein knockout studies: Analyzes N6-methyl-adenosine-associated gene expression after knocking out reader proteins.
• Demethylase inhibitor evaluation: Explores effectiveness of demethylase FTO inhibitors.
• Drug abuse research: Investigates histone-associated modifications in drug abuse in animals.

Methodology:

The evaluation is based on the cumulative distribution function and the statistical significance in differential expression of genes grouped by the number of 'epi-marks'.