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

Background: Microarrays allow genome-wide assays of gene expression. There is a need for userfriendly
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 immunesystem
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.