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

M.F.W. te Pas; S. van Hemert; B. Hulsegge; A.J.W. Hoekman; M.H. Pool; J.M.J. Rebel; M.A. Smits

doi:10.1155/2008/719468

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

M.F.W. te Pas, S. van Hemert, B. Hulsegge, A.J.W. Hoekman, M.H. Pool, J.M.J. Rebel, M.A. Smits

Research output: Contribution to journal › Article › Academic › peer-review

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

Original language	English
Pages (from-to)	719468
Number of pages	7
Journal	Advances in Bioinformatics
Volume	2008
DOIs	https://doi.org/10.1155/2008/719468
Publication status	Published - 2008

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title = "A Pathway Analysis Tool for Analyzing Microarray Data of Species with Low Physiological Information",

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",

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AU - te Pas, M.F.W.

AU - van Hemert, S.

AU - Hulsegge, B.

AU - Hoekman, A.J.W.

AU - Pool, M.H.

AU - Rebel, J.M.J.

AU - Smits, M.A.

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