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

Prickett D, Watson M - BMC Proc (2009)

Bottom Line: Several pathways were significantly affected based on the unadjusted p-value, including several immune-system pathways.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Group, Institute for Animal Health (IAH), Compton, Newbury, RG20 7NN, UK. dennis.prickett@bbsrc.ac.uk

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.

No MeSH data available.


Up- and down- regulated pathways. Heatmap of up- and down- regulated pathways using an unadjusted p-value cut-off of p <= 0.05. Red signifies up-regulation, green down-regulation and yellow indicates the pathway was both up- and down- regulated. White indicates no significance for that pathway in that experiment.
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Figure 2: Up- and down- regulated pathways. Heatmap of up- and down- regulated pathways using an unadjusted p-value cut-off of p <= 0.05. Red signifies up-regulation, green down-regulation and yellow indicates the pathway was both up- and down- regulated. White indicates no significance for that pathway in that experiment.

Mentions: Using an adjusted p-value cut-off of 0.05, two pathways, "ribosomal proteins" (PM8 and MA8) and small ligand GPCRs (PM8), were significantly affected. Using an unadjusted p-value cut-off of 0.05, 18 pathways were significantly affected in one or more experiments (Figure 2).


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

Prickett D, Watson M - BMC Proc (2009)

Up- and down- regulated pathways. Heatmap of up- and down- regulated pathways using an unadjusted p-value cut-off of p <= 0.05. Red signifies up-regulation, green down-regulation and yellow indicates the pathway was both up- and down- regulated. White indicates no significance for that pathway in that experiment.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2712750&req=5

Figure 2: Up- and down- regulated pathways. Heatmap of up- and down- regulated pathways using an unadjusted p-value cut-off of p <= 0.05. Red signifies up-regulation, green down-regulation and yellow indicates the pathway was both up- and down- regulated. White indicates no significance for that pathway in that experiment.
Mentions: Using an adjusted p-value cut-off of 0.05, two pathways, "ribosomal proteins" (PM8 and MA8) and small ligand GPCRs (PM8), were significantly affected. Using an unadjusted p-value cut-off of 0.05, 18 pathways were significantly affected in one or more experiments (Figure 2).

Bottom Line: Several pathways were significantly affected based on the unadjusted p-value, including several immune-system pathways.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Group, Institute for Animal Health (IAH), Compton, Newbury, RG20 7NN, UK. dennis.prickett@bbsrc.ac.uk

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.

No MeSH data available.