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This article is part of the supplement: EADGENE and SABRE Post-analyses Workshop

Open Access Research

Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria

Dennis Prickett* and Michael Watson

Author Affiliations

Bioinformatics Group, Institute for Animal Health (IAH), Compton, Newbury, RG20 7NN, UK

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BMC Proceedings 2009, 3(Suppl 4):S7  doi:10.1186/1753-6561-3-S4-S7

Published: 16 July 2009

Abstract

Background

Microarrays allow genome-wide assays of gene expression. There is a need for user-friendly software to visualise and analyse these data. Analysing microarray data in the context of biological pathways is now common, and several tools exist.

Results

We describe the use of MAPPFinder, a component of GenMAPP to characterise the biological pathways affected in chickens infected with the protozoan parasite Eimeria. Several pathways were significantly affected based on the unadjusted p-value, including several immune-system pathways.

Conclusion

GenMAPP/MAPPFinder provides a means to rapidly visualise pathways affected in microarray studies. However, it relies on good genome annotation and having genes reliably linked to pathway objects. We show that GenMAPP/MAPPFinder can produce useful results, and as the annotation of the chicken genome improves, so will the level of information gained.