m6A-express

m6A-express predicts condition-specific m6A regulation of gene expression from limited methylated RNA immunoprecipitation sequencing (MeRIP-seq) data to identify m6A sites that influence gene expression across cells, treatments, and tissues.

Key Features:

• Algorithmic approach: Predicts condition-specific m6A regulation of gene expression (m6A-reg-exp) from limited MeRIP-seq data.
• High predictive accuracy: Validated on simulated and real datasets, demonstrating high specificity and sensitivity.
• Robustness with limited data: Maintains performance with few MeRIP-seq samples and outperforms traditional log-linear models under limited-sample conditions.

Scientific Applications:

• Gene expression regulation insight: Elucidates competitive regulation by m6A writers METTL3 and METTL14 of condition-specific m6A-reg-exp across different genes in HeLa cells.
• Cell type-specific insights: Identifies METTL3-induced distinct m6A-reg-exp patterns in HepG2 cells that affect protein functions and stress-related processes.
• Tissue-specific patterns: Detects unique m6A-reg-exp patterns in human brain and intestine tissues, revealing enrichment in organ-specific processes.

Methodology:

Analyzes limited MeRIP-seq data with an algorithmic approach to predict condition-specific m6A-reg-exp and identify m6A sites relevant to varying cellular or treatment conditions.