MSU Superfund Projects and Cores:

Project 1: Characterization of the Pathways Linking Ah Receptor Activation with Altered B Cell Differentiation Using an Integrated Experimental and Computational Modeling Approach

Project 2: Dissecting the Signaling Network for Ah Receptor-mediated Bcell Toxicity

Project 3: Non-Additive Ah Receptor Ligand Interactions

Project 4: Influence of Ah Receptor Ligands on Inflammatory Responses: Consequences for Tissue Injury and Gene Expression

Project 5: A Proteomic Analysis of the AHR signaling Network

Project 6: Molecular Insight into Polyaromatic Toxicant Degradation by Microbial Communities

Project 7: Geochemical Controls on the Adsorption, Bioavailability, and Long-term Environmental Fate of Dioxins, PCBs, and PAHs

Core A: Administration

Core B: Research Translation

Core C: Computational Modeling of Mammalian Biomolecular Response

Core D: Biomedical Informatics

Core E: Environmental Molecular Analysis

Return to the MSU Superfund Main Page

Link to the NIEHS SBRP site

Superfund Core D: Biomedical Informatics

An integrated approach for investigating the biomolecular responses to Ahr ligands necessitates the application of modern genomic and proteomic tools. By utilizing these tools, the individual projects will be generating significant amounts of data that must be managed, stored, analyzed, and mined in order to derive knowledge from the mass of information. The Biomedical Informatics Core (BIC) was formed to perform these functions. 

The figure below illustrates general data flow within the Biomedical Informatics Core (BIC). The BIC located at MSU will be the initial point of analysis for all cDNA microarray experiments while CIIT will be the initial point of analysis for Affymetrix microarrays and the TAP protein interaction data.  The data will be mirrored at both sites allowing easy access by the biomedical investigators for data visualization and statistical analysis.

The primary mission of the BIC is to enable the biomedical investigators to derive optimal use of genomic and proteomic data in the most efficient manner possible. To obtain this goal, the general philosophy of the BIC is that responsibility for data interpretation should reside with the individual investigators since they are the experts in the biological systems in which they are studying. Our responsibility as a core is to provide consistent preliminary data analysis, software tools, data management infrastructure, and training necessary for their success. 

This mission will be implemented through the following specific aims: 

1. develop the infrastructure necessary to manage and store microarray and tandem affinity purification (TAP) data;

2. perform initial microarray data analysis for biomedical investigators and provide commercial and custom software tools for the visualization and analysis of microarray and TAP data; and

3. provide training and support to all biomedical investigators on the application and utilization of the software tools in relation to their specific analysis needs. 

For the large, complex datasets present in genomic and proteomic studies, the visual and intuitive capabilities of individual investigators must be coupled with computational analysis in order to recognize important patterns within the data. Establishing the BIC will insure a central repository will exist for all gene expression and TAP data and will enable efficient data mining to occur within and across projects.

Russell S. Thomas, Ph.D.
Core Leader
Hamner Institutes for Health Sciences

Timothy R. Zacharewski, Ph.D.
Co-Investigator
Michigan State University