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We have built a comprehensive Protein-Protein Interaction (PPI) network for human by aggregating and integrating PPI and other interaction data from several publicly available resources. We are able to filter this custom network based on a variety of criteria including gene expression, mutational patterns, phenotype, disease, and functional annotation, enabling a wide range of interaction network analyses. Moreover, we can overlay a variety of annotations onto the network. We can use these analyses to generate functional hypotheses for genes with limited functional information and to derive a pathway/module for a group of related genes-products involved in a common process.