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United States Department of Agriculture

Agricultural Research Service

Research Project: ASSOCIATION OF IMPRINTED GENES WITH REPRODUCTIVE EFFICIENCY IN SWINE Title: Annotation of Affymetrix Porcine Genome Microarray Chip

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: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: December 1, 2005
Publication Date: January 14, 2006
Citation: Tsai, S., Weir, B., Cassady, J., Freking, B.A., Nonneman, D.J., Rohrer, G.A., Piedrahita, J. 2006. Annotation of affymetrix porcine genome microarray chip. Plant and Animal Genome Conference Proceedings. Poster #P768. p. 292.

Technical Abstract: The newly available Affymetrix Porcine (AP) arrays are at present minimally annotated. Difficulties when attempting to interpret the biological relevance of AP results without reliable annotation prompted us to annotate the AP arrays utilizing probe set target sequences. Using the target sequence for each probe set we retrieved, where available, the corresponding porcine TIGR consensus sequence from the TIGR Porcine (Sus Scrofa) Gene Index (SsGI). The TIGR consensus sequence and the original target sequence were separately BLASTed against human cDNA and genomic sequence databases obtained from EnsEMBL. We verified that BLAST results using these longer TIGR consensus sequences were highly concordant with the shorter original target sequences (96.99% concordance in probes where target sequence BLAST against cDNA had bit score greater than 50). Overall, 85% of the probes could be annotated using the cDNA database. The assignments of annotations to these probes from the cDNA sequence database should be treated with a higher confidence than those probes sets that were assigned on the basis of the genomic database. In summary a total of 23,946 probes were annotated by this method and assigned EnsEMBL gene IDs. Of those 17,050 had high-confidence bit scores (>50 against EnsEMBL cDNA). Assignment of the remaining probes will require further assembly of TIGR contigs and/or sequencing of the porcine genome. This annotation is freely available via the web. http://brc.statgen.ncsu.edu/~tsai/annotation This project was supported by National Research Initiative Grant no. 2005-35604-15343 from the USDA Cooperative State Research, Education, and Extension Service to JP and BF.

Last Modified: 12/28/2014
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