title: Facilitating functional annotation of chicken microarray data.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA. tbuza@cvm.msstate.edu
authors.forename: Teresia J
authors.initials: TJ
authors.lastname: Buza
authors.forename: Ranjit
authors.initials: R
authors.lastname: Kumar
authors.forename: Cathy R
authors.initials: CR
authors.lastname: Gresham
authors.forename: Shane C
authors.initials: SC
authors.lastname: Burgess
authors.forename: Fiona M
authors.initials: FM
authors.lastname: McCarthy
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D030541:Databases, Genetic; D016678:Genome; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis