You are here: home » Oceans and Human Health » Marine Genomics » Bioinformatics Project
Bioinformatics Project
Project Goal
The role of the Bioinformatics project is to provide advanced computational analyses for data generated by the Applied Genomics Program and to collaborate with the Hollings Marine Laboratory (HML) data management section to integrate marine genomics data and synthesis (bioinformation) products into the overall activities of the NOAA Center of Excellence for Oceans and Human Health at the HML. The motivation for these specialized analysis activities is:
- The complexity and structure of the genomics data which precludes the application of traditional statistics as a data mining tool; and
- The need to integrate the genomics data and their analysis products with other programs at the NOAA Center of Excellence for Oceans and Human Health at the HML.
Learn more about the background information for this project »
Click here for a full project report
Abstract
The basic tools and methods have been developed for interrogating microarray data to extract the important signals and predict organism responses to a variety of stressors. In addition insights into the biology of metal accumulation in oyster and the value of various measure of toxicity have been explored.
Short-Term Objectives
The project objectives are to:
- Apply non-linear approaches to develop mathematical models of gene expression profiles generated by the Functional Genomics Research and the Marine Organisms as Disease Vectors projects for the oysters, Crassostrea virginica and C. gigas, and their pathogen, Perkinsus marinus;
- Develop similar analysis models for mapping transcript profiles of oysters to the other environmental data collected by the Oceans and Human Health program at the Hollings Marine Laboratory; and
- Identify genes (from 1 and 2 above) that appear to be significantly up- or down-regulated by the environmental conditions to which the oysters have been exposed.
Expected Results
The major product of the Bioinformatics project will be development of the analysis tools and approaches required to apply the functional genomics paradigm and integrate molecular- to organism-level information into assessments of the health status of marine ecosystems. In collaboration with the Marine Organisms as Disease Vectors project, the Bioinformatics and Functional Genomics Research projects will link the health status of oysters to human health risk resulting from bioaccumulation of human pathogens.
Accomplishments:
The BioInoformatic core has just received the necessary microarray data to begin working with the large data set generated by the Functional genomics section. These data have been examined for relationships between environmental exposure levels on the accumulation in tissues of three metals Cd. Cu and Zn. The results indicate that there is little correlation between exposure and accumulation of Cu and Zn, but a strong correlation exits for Cd. However, the Cd accumulation in tissues is dependent more on the length of exposure than on environmental concentrations. In the figure to the right, the sensitivities of the concentration of the three metals in gill and hepatopancreas tissues to exposure time and exposure levels are illustrated. These data were generated by 30 runs of an Artificial Neural Network and exposure time accounted for more than 40% of the variation in tissue concentrations. Further analysis of these were conducted by withholding 20 samples from each ANN run and then using the models to predict the tissue concentration of each metal. In the figure below the average correlations between the observed data and predictions are shown. Here, it is evident that only Cd can be predicted with reasonable accuracy.
In a related experiment conducted by Drs. Matt Jenny and Charlie Cunningham, oysters were challenged by a bacterial treatment and tissue samples taken from microarray analysis. These microarrays were compared to those from notched individuals and saline injected individuals. In the analysis we developed an approach for reducing the number of transcripts necessary to discriminate individuals in each treatment. The process began by assessing the sensitivity of discrimination for each transcript with a single pass through an ANN. The highest ranking transcripts (200) were taken for an addition 30 runs of the program for each treatment class. In the figure below a Receiver Operating Characteristic curve (ROC) demonstrates that correct classification of individuals subjected to bacterial challenge (24 hr post injection) can be achieved 94% of the time. False positives and false negatives comprise less than 6% of the data.
In addition to providing accurate predictions of bacterial challenge, this procedure reduced the number of transcripts to models the outcomes from 7000 to 200 and accelerated the processing time from days to hours with little or no degradation in the signal.
With the assistance of Dr. Jonas Almeida, the Marine Genomics Staff has developed a web accessible Microarray pipeline. The tool filters “bad” spots on the replicate Microarrays, normalizes the quantiles and spots, compares the genes on each Microarray to determine differential gene expression and returns a cumulative list of genes categorized by their level of regulation in the presence of stressos. Registered curators can analyze their data using the following statistical functions made available to them:
- Array data easy retrieval to MATLAB
- Array 'bad-spot' filtering
- Within-array calibration
- Spearman/Pearson values
- Differential expression values determination
- Array clustering
- Excel report generation of all values including differential values, p-values, fold difference values between spots across arrays etc.
- graphical reports
- Principle component analysis
Transfer of Results
The following products of genomics and bioinformatics research will be transferred as appropriate to user groups as stages in their development are complete.
| Deliverables | User Group |
|---|---|
| Annotated physical clone collections of oyster ESTs | Genomics research community, oyster aquaculture and selective breeding program and potentially pharmaceutical firms |
| Validated oyster⁄Perkinsus microarrays | Oyster research community and potentially biotechnology companies producing commercial microarrays |
| Oyster genes responsive to single and multiple stressors | Oyster research community, shellfish biologists, biotechnology companies and public health officials and agencies |
| Scientific articles relating to “Ecogenomics” | Bioinformatics and ecology researchers |
| Transcriptomic tools for assessing the health of the marine environment | Ocean ecosystem managers and wildlife management agencies |
Publications:
Robert W. Chapman. Javier Robalino, and Hal Trent. (2006) EcoGenomics: Analysis of Complex Systems Using Fractal Geometry. Integrative and Comparative Biology. Published on line May 2006
Public Information and Outreach:
The marine genomics website provides a publicly accessible database and set of analytical tools for understanding the genomics of selected marine organisms (including the American oyster, Atlantic white shrimp, grass shrimp and the Atlantic bottlenose dolphin) and assessing their health using transcriptomic methods. In addition the models developed from the analysis of the oyster data will become available over our web site in the future and accessible to researchers wishing to use them.
For More Information
Contact: Bob Chapman, (843) 762.8860
Email: chapmanr@dnr.sc.gov