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Exploration and analysis the interactome networks at systems level requires the integration and unification of the biomolecular elements and annotations that come from many different high-throughput or small-scale proteomic experiments, providing a non-redundant and correct identification of proteins and interactions. APID2NET is an open access tool fully integrated in Cytoscape that allows to surf unified interactome data by quering APID server (http://bioinfow.dep.usal.es/apid/) 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: 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 including all Cytoscape capabilities, plus new tools to automatic find and locate concurrent functional and structural attributes along all protein pairs in a network. A hubs location tool is also implemented. The use of protein annotation co-occurrence discovery is a neat way to improve our understanding of interactome networks.
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