FunDMDeep-m6A

FunDMDeep-m6A identifies differential N6-methyladenosine (m6A) methylation sites and prioritizes functional differential m6A methylation genes (FDmMGenes) at single-base resolution from MeRIP-Seq data.

Key Features:

• DMDeep-m6A Differential Site Detection: Integrates deep learning models with statistical tests to detect differential m6A methylation (DmM) sites from MeRIP-Seq data at single-base resolution.
• Network-Based Gene Prioritization: Combines differential expression analysis with a protein–protein interaction (PPI) network approach using an m6A-signaling bridge (MSB) score computed via heat diffusion to prioritize FDmMGenes.

Scientific Applications:

• Context-Specific m6A Functional Analysis: Identifies m6A-regulated genes across biological contexts such as stem cell differentiation, cancer, and disease versus normal comparisons, with downstream functional enrichment analysis.

Methodology:

FunDMDeep-m6A first applies DMDeep-m6A to detect DmM sites from MeRIP-Seq data using deep learning and statistical testing, then integrates differential expression results with PPI network analysis and MSB heat diffusion scoring to prioritize functionally significant FDmMGenes.