Bioinformatics Software for Proteomics Research

The overall objective of this project is to develop an innovative bioinformatics software to aid in the analysis and interpretation of proteomics data. The software is capable of quantifying and interpreting complex and time-dependent global changes in various biological pattern profiles. It will identify the links between protein expression changes with upstream and downstream events in the context of biological pathways and phenotypic outcome. Phase II effort will be focused on developing the software prototype. Protein expression and post-translational modification data such as protein arrays, LC/MS and gel electrophoresis (1-D or 2-D) data will be used as input for identification of protein expression changes. The proteomics data will be integrated with either gene expression data or metabolomics (metabonomics) data or both to identify the molecular events up- and down-stream of these protein changes in the pathways involved in the cellular response to the external insults. Existing information in publicly available literature and databases will be incorporated into the software in terms of a knowledge base. Once the entire data analysis/biological interpretation process is complete, the biological implications of the biomolecular changes will be provided, as well as the prediction of the likely outcome.