Developing Bioinformatics Tools for Proteomics Research

In Phase II, we propose to build the working “beta” version of MetaProt – the first functional data mining system focused on proteomics. The system will enable importing proteomics and complimentary OMICs data from different sources; mapping the data on biological pathways, networks and processes; pathway-based comparison between different datasets; and identification of condition-specific functional modules. MetaProt will be based on our integrated data mining suit, MetaCore, the leading systems biology platform licensed by over 100 accounts, including the largest pharmaceutical companies. MetaProt tools will work on the underlying manually curated database of high fidelity protein-protein, protein-DNA and protein-compound interactions collected at GeneGo from “small scale” experimental data. In Phase I, we have prototyped the algorithms, developed key changes in the database architecture and interface for MetaProt, developed a novel method for dataset comparison and conducted case studies on its utility. In Phase II, we will implement these developments in a stand alone web based enterprise system, fully functional and integrated with complimentary third party products including proteomics software, application integration platforms and translational medicine databases. MetaProt will be directly applicable in basic proteomics and systems biology research and in multiple areas of drug discovery.