Advances in Bioinformatics 
Volume 2008 (2008), Article ID 719468, 7 pages
doi:10.1155/2008/719468
Research Article

A Pathway Analysis Tool for Analyzing Microarray Data of Species with Low Physiological Information

M. F. W. te Pas,1 S. van Hemert,2 B. Hulsegge,1 A. J. W. Hoekman,1 M. H. Pool,1 J. M. J. Rebel,2 and M. A. Smits1

 1Animal Breeding and Genetics Centre (ABGC), Animal Sciences Group, Wageningen University and Research Centre, P.O. Box 65, 8200 AB, Lelystad, The Netherlands
2Department of Infectious Biology, Animal Sciences Group, Wageningen University and Research Centre, P.O. Box 65, 8200 AB, Lelystad, The Netherlands
Received 18 February 2008; Revised 25 July 2008; Accepted 17 October 2008

Recommended by Pierre Rouzé

Abstract

Pathway information provides insight into the biological processes underlying microarray data. Pathway information is widely available for humans and laboratory animals in databases through the internet, but less for other species, for example, livestock. Many software packages use species-specific gene IDs that cannot handle genomics data from other species. We developed a species-independent method to search pathways databases to analyse microarray data. Three PERL scripts were developed that use the names of the genes on the microarray. (1) Add synonyms of gene names by searching the Gene Ontology (GO) database. (2) Search the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database for pathway information using this GO-enriched gene list. (3) Combine the pathway data with the microarray data and visualize the results using color codes indicating regulation. To demonstrate the power of the method, we used a previously reported chicken microarray experiment investigating line-specific reactions to Salmonella infection as an example.