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BMC bioinformatics2009; 10 Suppl 11(Suppl 11); S8; doi: 10.1186/1471-2105-10-S11-S8

Structural and functional-annotation of an equine whole genome oligoarray.

Abstract: The horse genome is sequenced, allowing equine researchers to use high-throughput functional genomics platforms such as microarrays; next-generation sequencing for gene expression and proteomics. However, for researchers to derive value from these functional genomics datasets, they must be able to model this data in biologically relevant ways; to do so requires that the equine genome be more fully annotated. There are two interrelated types of genomic annotation: structural and functional. Structural annotation is delineating and demarcating the genomic elements (such as genes, promoters, and regulatory elements). Functional annotation is assigning function to structural elements. The Gene Ontology (GO) is the de facto standard for functional annotation, and is routinely used as a basis for modelling and hypothesis testing, large functional genomics datasets. Results: An Equine Whole Genome Oligonucleotide (EWGO) array with 21,351 elements was developed at Texas A&M University. This 70-mer oligoarray was designed using the approximately 7 x assembled and annotated sequence of the equine genome to be one of the most comprehensive arrays available for expressed equine sequences. To assist researchers in determining the biological meaning of data derived from this array, we have structurally annotated it by mapping the elements to multiple database accessions, including UniProtKB, Entrez Gene, NRPD (Non-Redundant Protein Database) and UniGene. We next provided GO functional annotations for the gene transcripts represented on this array. Overall, we GO annotated 14,531 gene products (68.1% of the gene products represented on the EWGO array) with 57,912 annotations. GAQ (GO Annotation Quality) scores were calculated for this array both before and after we added GO annotation. The additional annotations improved the meanGAQ score 16-fold. This data is publicly available at AgBase http://www.agbase.msstate.edu/. Conclusions: Providing additional information about the public databases which link to the gene products represented on the array allows users more flexibility when using gene expression modelling and hypothesis-testing computational tools. Moreover, since different databases provide different types of information, users have access to multiple data sources. In addition, our GO annotation underpins functional modelling for most gene expression analysis tools and enables equine researchers to model large lists of differentially expressed transcripts in biologically relevant ways.
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Publication Date: 2009-10-08 PubMed ID: 19811692PubMed Central: PMC3226197DOI: 10.1186/1471-2105-10-S11-S8Google Scholar: Lookup
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  • Journal Article
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article discusses the creation and annotation of an Equine Whole Genome Oligonucleotide (EWGO) array, which helps in understanding the equine genome and deriving value from genomics datasets. The researchers have structurally annotated the array, mapping elements to key databases, and have provided Gene Ontology (GO) functional annotations for gene transcripts represented on the array.

Creation of the Equine Whole Genome Oligonucleotide (EWGO) Array

  • The researchers at Texas A&M University, leveraging the sequenced equine genome, developed an EWGO array with 21,351 elements.
  • This 70-mer oligoarray was designed using the assembled and annotated sequence of the equine genome, representing one of the most comprehensive arrays for equine sequences.

Structural Annotation of the EWGO Array

  • The team performed structural annotation on the array, which is the process of delineating and demarcating the genomic elements such as genes, promoters, and regulatory elements.
  • The elements of the array were mapped to multiple database accessions including UniProtKB, Entrez Gene, NRPD (Non-Redundant Protein Database) and UniGene.

Functional Annotation of the EWGO Array and Results

  • Functional annotation, assigning function to structural elements, was carried out using the Gene Ontology (GO), a standard system for these annotations.
  • The researchers provided GO functional annotations for the gene transcripts represented on this array.
  • From the array’s total, 14,531 gene products (which constitute 68.1% of the gene products) were annotated with 57,912 annotations.
  • The quality of the annotations was evaluated using the GAQ (GO Annotation Quality) scores both before and after adding the GO annotation, showing a 16-fold improvement in the mean GAQ score after adding the annotations.

Conclusion and Implications

  • The additional information provided about the public databases, linked to the gene products on the array, offers users a greater flexibility when using computational tools for gene expression modelling and hypothesis testing.
  • By providing access to different types of information from different databases, it enhances the utility of the array for various research purposes.
  • The GO annotation aids functional modelling for most gene expression analysis tools, enabling researchers to model large lists of differentially expressed transcripts in biologically relevant ways.
  • The data derived from this research is publicly available, providing a valuable resource for equine researchers globally.

Cite This Article

APA
Bright LA, Burgess SC, Chowdhary B, Swiderski CE, McCarthy FM. (2009). Structural and functional-annotation of an equine whole genome oligoarray. BMC Bioinformatics, 10 Suppl 11(Suppl 11), S8. https://doi.org/10.1186/1471-2105-10-S11-S8

Publication

BMC bioinformatics
ISSN: 1471-2105
NlmUniqueID: 100965194
Country: England
Language: English
Volume: 10 Suppl 11
Issue: Suppl 11
Pages: S8

Researcher Affiliations

Bright, Lauren A
  • Department of Clinical Sciences, College of Veterinary Medicine, Mississippi State University, PO Box 6100, Mississippi State, MS, 39762, USA. lbright@cvm.msstate.edu.
Burgess, Shane C
    Chowdhary, Bhanu
      Swiderski, Cyprianna E
        McCarthy, Fiona M

          MeSH Terms

          • Animals
          • Databases, Genetic
          • Genome
          • Genomics / methods
          • Horses / genetics
          • Oligonucleotide Array Sequence Analysis / methods

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          Citations

          This article has been cited 9 times.
          1. Bright LA, Dittmar W, Nanduri B, McCarthy FM, Mujahid N, Costa LR, Burgess SC, Swiderski CE. Modeling the pasture-associated severe equine asthma bronchoalveolar lavage fluid proteome identifies molecular events mediating neutrophilic airway inflammation. Vet Med (Auckl) 2019;10:43-63.
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