Pathway Explorer

Pathway Explorer maps high-throughput gene and protein expression data onto curated biological pathways to enable pathway-centric interpretation of regulatory, metabolic, and cellular processes.

Key Features:

• Expression-to-pathway mapping: Maps gene and protein expression profiles onto pathway components to reveal pathway-level changes and implicated regulatory mechanisms and metabolic processes.
• Database integration: Leverages curated pathway resources including KEGG, BioCarta, and GenMAPP for pathway definitions and annotations.
• Pathway visualization and ranking: Generates color-coded overlays of expression values on pathway maps and ranks pathways by relevance according to user-specified or built-in criteria.
• Export formats: Produces pathway map outputs in PNG and JPG raster formats and SVG vector graphics for high-resolution and publication-quality figures.

Scientific Applications:

• Pathway-centric differential analysis: Identify key genes and proteins within specific pathways that are differentially expressed under experimental conditions.
• Regulatory and metabolic network exploration: Explore potential regulatory networks and metabolic alterations associated with diseases, treatments, or experimental perturbations.
• Hypothesis generation: Facilitate formulation of hypotheses about the biological significance of observed expression changes at the pathway level.

Methodology:

Systematic mapping of user-provided expression data onto curated pathway maps from KEGG, BioCarta, and GenMAPP, combined with a pathway ranking procedure based on specified relevance criteria.