Relational databases and pathway-assisted analysis of omics data
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- Research Group
- External Collaborators
Prof. Susumu Goto, Bioinformatics Center, Kyoto University, Japan
Prof. Alan R. Buckpitt, Dept. of Molecular Biosciences, University of California Davis, USA
Prof. Bruce D. Hammock, Department of Entomology and Cancer Research Center, University of California, Davis, USA
- Description
In this new era of “omics” technologies, relational databases have become a necessity for analysis of the large sets of data produced in global investigations of genomes, proteomes and metabolomes. These databases are vital in converting the omics from merely hypothesis generating research to hypothesis driven and mechanistically-based research. Furthermore, various database structures are becoming increasingly important in the understanding of the mechanisms underlying pathological processes. In addition, the utilization of a relational database structure makes possible not only more comprehensive analyses and evaluations of omics data than conventional analysis methods can afford, but also facilitates meta-analysis of multiple, related exposure studies.
In this project, we are developing an integrated database correlating the metabolomics and proteomics data generated from our studies of synergistic toxicological effects of two common ambient air pollutants; ozone and 1-nitronaphthalene. The project is performed in collaboration with Kyoto University Bioinformatics Center, the home of the Kyoto Encyclopedia of Genes and Genomes (KEGG). Visualization of alterations in expression patterns in the various affected KEGG pathways is an integral and essential part of the database. Use of the KegArray tool allows for simultaneous pathway analysis of different types of omics data, thus facilitating an overview of the biological alterations that occur in response to a given toxicant or disease. Upon completion, the resulting Pulmonomics database will be made available to the public, with the possibility to be expanded by additional lung toxicology studies. The database will be a key element in evaluating the validity of extrapolation of results from this rodent animal model to human subjects, as well as extrapolation between related classes of pneumotoxicants.
