Data Integration and Bioinformatics Core

Director: Judith Klein-Seetharaman, PhD

The Data Integration and Bioinformatics core is responsible for (1) the PCHPI website and the prediction web server, (2) rank ordering target molecules and complexes, and (3) facilitating iterative feed-back to and from each of the cores, the technology program and the collaborative projects.

The web server disseminates the tools and data developed and generated by the PCHPI. It supports collaborations between members of the PCHPI, as well as between the center and outside collaborators. Internal and external collaborators can follow their projects remotely.

The identification of protein binding partners is error-prone since high-throughput approaches yield incomplete and noisy information. Therefore, a functional linkage between putative binding partners should be established. Algorithms developed in the Data Integration and Bioinformatics Core take data from diverse biological sources and integrates the information. Input data is both direct (from yeast two-hybrid, co-immunoprecipitation, or mass-spectrometry studies) and indirect or implicit (based on gene expression profiles, annotation). . The algorithm output allows one (i) to have greater confidence that an identified interaction is real, (ii) to predict new interactions, and (iii) to generate hypotheses on the functional significance of an interaction. The Data Integration and Bioinformatics Core is actively developing this integrated approach to generate verifiable predictions of the human-HIV “interactome”.

To explore our rankings and predictions, please visit our interactive prediction lookup tool. Our approach and overall ranking / prediction results have been described in a recent publication:

Tastan O, Qi Y, Carbonell, JG, and Klein-Seetharaman, J. "Prediction of Interactions Between HIV-1 and Human Proteins by Information Integration", Pacific Symposium on Biocomputing, Big Island of Hawaii, January 5-9, 2009.