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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.


Distribution of pathway coverage in GenMAPP. The histogram shows the log2 of the ratio of number of genes mapped to total number of genes on the pathway. The majority of pathways have a value greater than 0.5, which represents a figure of 50% of genes in the pathway are mapped to probes on the array.
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Figure 1: Distribution of pathway coverage in GenMAPP. The histogram shows the log2 of the ratio of number of genes mapped to total number of genes on the pathway. The majority of pathways have a value greater than 0.5, which represents a figure of 50% of genes in the pathway are mapped to probes on the array.

Mentions: The distribution of the ratio of genes mapped to total genes in the pathway is shown in Figure 1 and has a mean of 0.67. This shows that in most cases the majority of the entities in a pathway are represented in the data by at least one gene.


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

Prickett D, Watson M - BMC Proc (2009)

Distribution of pathway coverage in GenMAPP. The histogram shows the log2 of the ratio of number of genes mapped to total number of genes on the pathway. The majority of pathways have a value greater than 0.5, which represents a figure of 50% of genes in the pathway are mapped to probes on the array.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Distribution of pathway coverage in GenMAPP. The histogram shows the log2 of the ratio of number of genes mapped to total number of genes on the pathway. The majority of pathways have a value greater than 0.5, which represents a figure of 50% of genes in the pathway are mapped to probes on the array.
Mentions: The distribution of the ratio of genes mapped to total genes in the pathway is shown in Figure 1 and has a mean of 0.67. This shows that in most cases the majority of the entities in a pathway are represented in the data by at least one gene.

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.