ArticleBMC bioinformatics2009
Facilitating functional annotation of chicken microarray data.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Article
- Inter-Species Host Gene Expression Differences in Response to Human and Avian Influenza A Virus Strains.International journal of molecular sciences · 2017Article
- Fetal and organ development at gestational days 45, 90, 135 and at birth of lambs exposed to under- or over-nutrition during gestationTranslational animal science · 2017Article
- Experimental approaches for gene regulatory network construction: the chick as a model system.Genesis (New York, N.Y. : 2000) · 2013Review
- Transcriptome analysis in chicken cecal epithelia upon infection by Eimeria tenella in vivo.PloS one · 2013Article
- AgBase: supporting functional modeling in agricultural organisms.Nucleic acids research · 2011Article
- Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference.BMC bioinformatics · 2010Article
- Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction.BMC bioinformatics · 2009Article
- Structural and functional-annotation of an equine whole genome oligoarray.BMC bioinformatics · 2009Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundModeling 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.
resultsWe 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.
conclusionResults 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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