CellWhere: graphical display of interaction networks organized on subcellular localizations

Area of Science:

• Cell biology
• Bioinformatics
• Systems biology

Background:

• Understanding protein function requires knowledge of both interactions and subcellular localization.
• Existing tools often analyze these aspects separately, limiting holistic biological insights.

Purpose of the Study:

• To develop CellWhere, an interactive tool for visualizing protein-protein interactions within subcellular locations.
• To facilitate hypothesis generation by integrating protein localization and interaction data.

Main Methods:

• CellWhere utilizes public databases like Gene Ontology and UniProt for subcellular localization data.
• Protein-protein interaction data is sourced from the Mentha interactome server or user-uploaded networks.
• The Cytoscape.js library generates interactive graphical displays of cellular networks.

Main Results:

• CellWhere provides a user-friendly interface to explore gene and protein interaction networks organized by subcellular location.
• The tool allows prioritization of specific subcellular locations for proteins found in multiple compartments.
• It enables simultaneous exploration of protein localization and interaction data.

Conclusions:

• CellWhere enhances biological research by offering an integrated view of protein localization and interactions.
• The tool empowers experimental biologists to formulate more informed mechanistic hypotheses.
• CellWhere serves as a valuable resource for exploring complex cellular systems.