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United States Department of Agriculture

Agricultural Research Service

Research Project: ASSOCIATION OF IMPRINTED GENES WITH REPRODUCTIVE EFFICIENCY IN SWINE

Location: Reproduction Research

Title: Annotation of the Affymetrix Porcine Genome Microarray

Authors
item Tsai, S. - NORTH CAROLINA STATE UNIV
item Weir, B. - NORTH CAROLINA STATE UNIV
item Cassady, J. - NORTH CAROLINA STATE UNIV
item Freking, Bradley
item Nonneman, Danny
item Rohrer, Gary
item Piedrahita, J. - NORTH CAROLINA STATE UNIV

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 31, 2006
Publication Date: August 1, 2006
Citation: Tsai, S., Cassady, J.P., Freking, B.A., Nonneman, D.J., Rohrer, G.A., Piedrahita, J.A. 2006. Annotation of the affymetrix porcine genome microarray. Animal Genetics. 37:423-424.

Interpretive Summary: A porcine-specific microarray has been developed from publicly available sequence data by Affymetrix and provided to the research community interested in evaluating transcript expression levels. Less than 10% of the probe sets on this array were described with gene names, posing a challenge to biological interpretation of data. Lack of annotation is likely due to limited availability of information describing the full length of each porcine gene represented. A strategy for improving annotation of this microarray and its results were presented and made available to the research community on the web. The improved annotation for the Affymetrix Porcine microarray now describes approximately 82% of the probe sets. This annotation should greatly increase the usefulness of Affymetrix Porcine arrays for gene expression studies.

Technical Abstract: The Affymetrix Porcine Genome Microarray is minimally annotated. Less than 10% of the probe sets on this array are described with gene names, posing a challenge to biological interpretation of data. Lack of annotation is likely due to limited availability of full-length porcine cDNA sequence. Presented here is a strategy for improving annotation of this microarray and its results. This annotation is available for download as a supplement to this article and at http://www4.ncsu.edu/~stsai2/annotation.

Last Modified: 4/21/2014