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Published on: January 30, 2017
Structural and functional-annotation of an equine whole genome oligoarray
Lauren A Bright1, Shane C Burgess, Bhanu Chowdhary
1Department of Clinical Sciences, College of Veterinary Medicine, Mississippi State University, PO Box 6100, Mississippi State, MS, 39762, USA. lbright@cvm.msstate.edu.
BMC Bioinformatics
|October 9, 2009
Summary
This study enhanced the Equine Whole Genome Oligonucleotide array by adding functional Gene Ontology (GO) annotations. This improves biological modeling and hypothesis testing for equine researchers using gene expression data.
Area of Science:
- Genomics
- Bioinformatics
- Equine Science
Background:
- The horse genome is sequenced, enabling high-throughput functional genomics.
- Effective use of genomics data requires comprehensive genome annotation.
- Gene Ontology (GO) is the standard for functional annotation.
Purpose of the Study:
- To structurally and functionally annotate the Equine Whole Genome Oligonucleotide (EWGO) array.
- To improve the biological relevance of functional genomics data analysis in horses.
- To provide enhanced annotation for equine gene expression studies.
Main Methods:
- Developed an Equine Whole Genome Oligonucleotide (EWGO) array.
- Structurally annotated array elements by mapping to multiple databases (UniProtKB, Entrez Gene, NRPD, UniGene).
- Provided Gene Ontology (GO) functional annotations for gene transcripts.
Main Results:
- GO annotated 14,531 gene products (68.1%) on the EWGO array with 57,912 annotations.
- The added GO annotations improved the GO Annotation Quality (GAQ) score 16-fold.
- Annotated data is publicly available at AgBase.
Conclusions:
- Enhanced annotation provides flexibility for gene expression modeling and hypothesis testing.
- Access to multiple databases through annotation offers diverse data sources.
- GO annotation enables biologically relevant functional modeling for equine gene expression analysis.
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