MethMotif Toolkit

MethMotif Toolkit integrates transcription factor binding site motifs with DNA methylation profiles to analyze methylation-sensitive transcription factors and their dimerization partners.

Key Features:

• TFregulomeR: An R package for visualizing methylation-specific transcription factor motifs and analyzing context-dependent and context-independent binding patterns.
• Forked-TF: An R library for characterizing leucine-zipper transcription factors that bind DNA as dimers, with a focus on dimerization partner identification and cofactor analysis.
• MethMotif Database Integration: Enables retrieval of ChIP-seq and DNA methylation data, intersection of transcription factor binding site peak regions, and generation of TFBS-methylation-informed motif logos.
• Dimerization Partner Exploration: Supports identification of transcription factor dimers and analysis of their co-binding behavior across cell types and conditions.

Scientific Applications:

• Methylation-Sensitive Transcription Factor Analysis: Investigates how DNA methylation modulates transcription factor binding specificity across different cell types and conditions.
• Leucine-Zipper Transcription Factor Characterization: Analyzes bZIP transcription factor binding patterns, dimerization partners, and cofactors in a cell-type-specific context.
• Gene Regulatory Network Investigation: Uncovers how DNA methylation and transcription factor dimerization influence gene regulatory networks.
• Alternative Cofactor Visualization: Enables visualization and analysis of alternative cofactors for transcription factor binding.

Methodology:

The toolkit integrates transcription factor binding site motifs with DNA methylation profiles through database retrieval of ChIP-seq and DNA methylation data, intersection of TFBS peak regions, and generation of TFBS-methylation-informed motif logos.