MotifLab

MotifLab integrates genomic and epigenomic data to discover transcription factor binding sites and cis-regulatory modules in regulatory sequence regions.

Key Features:

• Integration of Multiple Data Types: Incorporates phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, and positional binding preferences to prioritize functional motif candidates.
• Support for Various Motif Discovery Tools: Supports integration of outputs from multiple motif discovery tools to combine methodologies and improve prediction accuracy.
• Data-Processing Operations: Provides operations to create, manipulate, and analyze data objects and to construct and automatically execute complete analysis workflows.
• Graphical Presentation of Results: Generates graphical representations of analysis results for visualization of motifs and regulatory features.

Scientific Applications:

• Benchmarking motif discovery: Evaluated on benchmark datasets for single motifs and modules.
• Regulatory analysis of drug response: Applied to identify regulatory motifs in genes responding to forskolin treatment.
• Cell-type specific motif identification: Combines genome-wide chromatin accessibility and epigenetic state data to identify functional motifs in different cell types.

Methodology:

Incorporates positional priors and contextual biological data (phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq, positional binding preferences), supports running multiple motif discovery tools, and uses data-processing operations to construct and execute analysis workflows.