"This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5)."
The University of California, Santa Cruz is awarded a career-development grant to create new algorithms for discovering causal genetic interactions and extend the UCSC Interaction Browser, an online functional genomics resource for investigating networks of gene-associated relationships. Physical and regulatory gene interactions form the basis for many molecular mechanisms that govern the phenotypic output of cells. Cells respond to developmental programs or environmental queues using cascades of signals and molecular-level physical interactions. Characterizing such genetic wiring diagrams in normal and diseased cells is one of the next major challenges in molecular biology. The results of high-throughput approaches, most notably genome-wide expression data collected from DNA microarrays, are available in public repositories. It is critical to develop algorithms to discover functional and causal gene interactions underlying normal and disease processes from both observational and interventional data. The research carried out under this award will develop retrospective analyses based on network alignment and metaanalysis using data within and across species to identify gene-gene linkages that are general, specific to experimental contexts, conserved across different subsets of species, or present only in certain lineages of evolutionary history. The project will deliver online resource to allow researchers to superimpose their own experimental results with those inferred from published studies. This will provide a much-needed summation of the large collections of high-throughput functional genomics datasets to facilitate the interpretation of new datasets.
The resource will be made available through UCSC's web portal (http://genome.ucsc.edu/) so that the large research community of bioinformaticians and biologists that use the UCSC Genome Browser can access the Interaction Browser. Genetic networks determined from functional genomics studies or predicted from computational algorithms will be available for browsing and bulk downloading. The project will incorporate integrative network analysis topics into undergraduate- and graduate-level courses at UCSC. Three-dimensional displays at the San Francisco Exploratorium will enable students and the general public to visualize genetic networks, see how gene function can be predicted from network context, and investigate the evolution of gene interaction networks.
