Integration of genomic data for pharmacology and toxicology using Internet resources¶

¶Presented at CMTPI 2005: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Shanghai, China, October 29–November 1, 2005).

Abstract

Genome based technologies such as sequencing and gene expression profiling using microarrays are creating massive amounts of data. Results from these studies have provided unique insights into targets, biochemical pathways, and biological systems affected by drug or xenobiotic chemical treatments. Moreover, these genomic technologies offer the potential to identify biomarkers for pharmacological development or toxicological prediction. Nonetheless, microarray studies involving a single compound produce useful although limited data. To gain further power from these individual studies, the ability to combine datasets through integration schemes has become imperative. In the current study, we describe and analyze currently available Internet resources designed to address this problem. Many functionalities, such as ability to cross reference orthologous genes across species or to combine same technology platform data, are present in these resources. Nonetheless, these resources are limited in the number of technology platforms they can support. While the ability to integrate all currently existing gene expression datasets remains enigmatic, the current tools provide a partial solution that may still yield unique insights into the affects of exogenous molecules at the level of gene expression.

¶Presented at CMTPI 2005: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Shanghai, China, October 29–November 1, 2005).

Keywords:

• Genomic data
• Integration
• Bioinformatics
• Internet

Acknowledgements

The authors thank Jani Kekäläinen, Petri Pehkonen, Tom Kolmakow and Markus Storvik for discussions and helpful comments. The authors also wish to thank all the researchers who have taken part in making resources reviewed in this article available.

Notes

¶Presented at CMTPI 2005: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Shanghai, China, October 29–November 1, 2005).