MinePath

MinePath performs sub-pathway decomposition and differential analysis of gene regulatory networks to identify phenotype-associated regulatory sub-paths from gene expression data.

Key Features:

• Sub-pathway Decomposition: Decomposes canonical pathways into constituent sub-paths that capture regulatory relations and network topology rather than treating pathways as unordered gene sets, in contrast to traditional GSA approaches.
• Integration with Gene Expression Profiles: Matches regulatory sub-paths to gene expression sample profiles to evaluate functional activity and assess phenotype differential power.
• Significance Assessment and Ranking: Assesses statistical significance of pathways and sub-paths and ranks them by p-values.
• Molecular Relation Exploitation: Utilizes explicit gene-gene molecular relationships such as activation and inhibition to define functional sub-paths and detect differentially expressed pathway parts.
• Visualization of Regulatory Mechanisms: Visualizes regulatory mechanisms and functional sub-paths per phenotype with linked annotations for engaged genes and molecular relations.

Scientific Applications:

• Regulatory mechanism discovery: Reveal regulatory mechanisms underlying differential gene expression associated with specific phenotypes in biomedical research.
• GRN interpretation: Interpret gene regulatory networks to identify phenotype-differentiating regulatory sub-paths and the genes involved.
• Hypothesis generation and validation: Support exploratory molecular biology by uncovering key regulation within longer pathway sub-paths for downstream hypothesis generation and validation.

Methodology:

Decomposes pathways into sub-paths; matches regulation sub-paths with gene expression sample profiles to evaluate functional status and phenotype differential power; exploits exact gene-gene molecular relationships (activation and inhibition) and network topology to identify differentially expressed pathway parts; computes statistical significance and ranks results by p-values.