Exploration and analysis of interactome networks at systems level requires a unification of the biomolecular elements and annotations that come from many different high-throughput or small-scale proteomic experiments. Only such integration can provide a non-redundant and consistent identification of proteins and interactions. APID2NET is an open access tool, included in Cytoscape, that allows to surf unified interactome data by quering APID server and facilitates dynamic analysis of the protein-protein interaction (PPI) networks. The program is designed to visualize, dynamically explore and analyze the proteins and interactions retrieved, including all the annotations and attributes associated to such PPIs, i.e.: GO terms, Pfam and InterPro domains, experimental methods that validate each interaction, PubMed IDs, UniProt IDs, etc. The tool provides a rich interactive graphical representation of the networks with all Cytoscape capabilities, plus new automatic tools to find and locate concurrent functional and structural attributes along all protein pairs in a network. A hubs location tool is also implemented.
- Hernandez-Toro J., Prieto C. and De Las Rivas J. (2007). APID2NET: unified interactome graphic analyzer. Bioinformatics 23(18): 2495-2497. PMID: 17644818.