The Gene Ontology Annotation Quality Analysis in Model Eukaryotes
Buza, T., Wang, N., Bridges, S., McCarthy, F.M., & Burgess, S. (2008). The Gene Ontology Annotation Quality Analysis in Model Eukaryotes. Nucleic Acids Research. 36, 2.
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.