A Pathway Analysis Tool for Analyzing Microarray Data of Species with Low Physiological Information. (24th December 2008)

• Record Type: Journal Article
• Authors: te Pas, M. F. W.; van Hemert, S.; Hulsegge, B.; Hoekman, A. J. W.; Pool, M. H.; Rebel, J. M. J.; Smits, M. A.
• Other Names: Rouzé Pierre Academic Editor.
• Is Part Of: Advances in bioinformatics. Volume 2008(2008)
• Publication Date: 2008-12-24
• Subjects: Bioinformatics -- Periodicals; Bioinformatics; Computational Biology -- Periodicals; Periodicals; 570.285
• DOI: 10.1155/2008/719468
• Languages: English
• ISSNs: 1687-8027

Abstract

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.