Integrating Gene Expression Data, Protein Interaction Data, and Ontology-Based Literature Searches

Until recently, genomics and proteomics have commonly been separate fields that are studied and applied independently. We introduce the BioGrid4 platform, which aims to bridge this gap by integrating gene expression and protein interaction data. In the expression space, gene expression data can be analyzed using standard clustering techniques. To link the gene expression space with the protein interaction space, we assign domains and superfamilies to gene products by applying the SUPERFAMILY tool and the Structural Classification of Proteins (SCOP) database. For these proteins, the BioGrid platform may display possible physical interactions between them as predicted by the Protein Structure Interactome Map (PSIMAP). Any findings in the gene expression and protein interaction space should be compared with those reported in the scientific literature. Therefore both spaces are linked to a literature space by integrating GoPubMed, a system for ontology-based literature searches, into the BioGrid platform. We illustrate the approach that the BioGrid platform enables through an analysis of energy-related genes and protein complexes.