PINT

PINT integrates SBML pathway models and harmonizes model annotations to produce merged pathway diagrams that visualize gene- and expression-level data for systems biology analysis.

Key Features:

• Integration of SBML files: Handles standard SBML files from public databases and integrates multiple pathway models into a cohesive framework.
• Annotation editor: Provides an annotation editor to revise and harmonize component name inconsistencies across different models.
• Curated model collection: Includes approximately 190 curated public models of human pathways.
• Model querying: Enables selection of models based on specific criteria or gene lists derived from high-throughput experiments.
• Model integration and visualization (painting): Merges selected models into a combined pathway diagram and offers a painting function to highlight genes or expression levels on the merged pathway.

Scientific Applications:

• Systems biology analysis: Enables analysis of complex interactions within biological pathways by integrating multiple pathway models.
• Pathway-level interpretation of high-throughput data: Maps gene lists or expression data onto merged pathway diagrams to interpret results from high-throughput experiments.
• Hypothesis generation and testing: Supports hypothesis generation and testing by visualizing how genes or proteins interact within a pathway context.

Methodology:

Collection and curation of SBML files from public databases; upload or selection from the curated collection; resolving inconsistencies via annotation editing; merging selected models into a comprehensive diagram; and using the painting function to visualize specific genes or expression levels.