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. 2009 Oct 8;10 Suppl 11(Suppl 11):S2.
doi: 10.1186/1471-2105-10-S11-S2.

Facilitating functional annotation of chicken microarray data

Teresia J Buza  1 , Ranjit Kumar, Cathy R Gresham, Shane C Burgess, Fiona M McCarthy
Affiliations

Facilitating functional annotation of chicken microarray data

Teresia J Buza et al. BMC Bioinformatics. .

Abstract

Background: Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO). However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information.

Results: We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM) tool to help researchers to quickly retrieve corresponding functional information for their dataset.

Conclusion: Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and will be updated on regular basis.

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Figures

Figure 1
Figure 1
Functional annotation of Affymetrix chicken genome array. Original annotation of Affymetrix chicken array (grey bars) were compared with re-annotated GO (black bars). All biological ontologies show improvements realized from the re-annotation.
Figure 2
Figure 2
The mean GAQ score of the GO annotation. The mean GAQ scores are calculated for both original (black bar) and re-annotated (grey bar) GO annotations. The mean GAQ score is based only on the unique gene products with GO, not individual the probesets.
Figure 3
Figure 3
Types of genes and drug targets represented on Affymetrix GenChip® chicken genome array Sample figure title. The probesets matching different types of genes (A) were determined by using Ingenuity Pathway Analysis software. Some probesets were mapped to genes that are considered drug targets (B).
Figure 4
Figure 4
Distribution of genes and gene products represented on Affymetrix and Arizona chicken array.
See this image and copyright information in PMC

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