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Progress Reports: Duke University: Functional Genomics Research Core

Superfund Research Program

Functional Genomics Research Core

Project Leader: Joel N. Meyer
Grant Number: P42ES010356
Funding Period: 2005-2011

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Progress Reports

Year:   2008  2007  2006  2005 

Overview
The Functional Genomics Research Core (FGRC) provides support for multiple Superfund investigators engaged in microarray experimentation and analysis. Microarray experiments permit the genome-wide analysis and comparison of mRNA levels from multiple samples, thus providing a particularly powerful and data-rich approach to understanding the biological response to Superfund chemicals. However, there are technical challenges associated with carrying out microarray experiments, and useful analysis of the large datasets generated requires careful analysis. It is the mission of the FGRC to support SBRP projects that carry out microarray experiments by minimizing technical difficulties and facilitating data analysis.

Approaches
The FGRC consults with individual investigators on microarray experimental design. High-quality RNA is essential for good microarray experiments, and the FGRC provides technical laboratory support for assuring high-quality RNA. Microarray experiments are highly reproducible and comparable when carried out using consistent protocols and platforms (microarray slides). To assure high-quality results, the FGRC has contracted with Cogenics, an industry leader in microarray experiments, to carry out RNA amplification, labeling, microarray hybridization, scanning, and data extraction and acquisition. The FGRC supports the ability of SBRP project researchers to analyze gene expression data by setting up workshops, carrying out training activities, and arranging contractual bioinformatics services.

2008 activities
Arrays: A total of 626 arrays have been processed to date, with 308 processed in 2008 in support of Drs. Slotkin, Linney and Di Giulio.

Consultation and data analysis: Extensive consultations (Summer 2008) were held with Dr. Meyer, Dr. Lobenhofer, Dr. Di Giulio, and Lindsey Van Tiem for experimental design purposes. In 2008, significantly more time and effort were dedicated to data analysis. Dr. Slotkin’s research required an in-laboratory data analyst, and Drs. Linney and Di Giulio carried out data analysis in consultation with Cogenics (on a contractual basis). This additional analysis was made possible by the decrease in array cost that has occurred since the time of the original budgeting.

Training: Three workshops were held in Spring 2008 to train Superfund researchers (SBRP lab staff, graduate students and postdocs) in the use of three gene expression analysis tools: GeneSpring, GoMiner, and Cytoscape. GeneSpring is a bioinformatics software package for the visualization and analysis microarray expression data. GoMiner is a bioinformatics tool that permits analysis of microarray data from the perspective of gene ontologies. Genes are grouped according to gene ontology (biological function, molecular function, and cellular localization) and these groups of genes are analyzed in conjunction. Cytoscape maps gene expression data onto networks representing gene-gene and gene-protein interactions, allowing for the detection of altered “neighborhoods” representing groups of interconnected genes that are all changing.

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