title: Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation.
abstract: The design of oligonucleotide sequences for the detection of gene expression in species with disparate volumes of genome and EST sequence information has been broadly studied. However, a congruous strategy has yet to emerge to allow the design of sensitive and specific gene expression detection probes. This study explores the use of a phylogenomic approach to align transcribed sequences to vertebrate protein sequences for the detection of gene families to design genomewide 70-mer oligonucleotide probe sequences for bovine and porcine. The bovine array contains 23,580 probes that target the transcripts of 16,341 genes, about 72% of the total number of bovine genes. The porcine array contains 19,980 probes targeting 15,204 genes, about 76% of the genes in the Ensembl annotation of the pig genome. An initial experiment using the bovine array demonstrates the specificity and sensitivity of the array.
authors.affiliation: Department of Animal Science, University of Minnesota, St Paul, MN 55108, USA.
authors.forename: John R
authors.initials: JR
authors.lastname: Garbe
authors.forename: Christine G
authors.initials: CG
authors.lastname: Elsik
authors.forename: Eric
authors.initials: E
authors.lastname: Antoniou
authors.forename: James M
authors.initials: JM
authors.lastname: Reecy
authors.forename: Karl J
authors.initials: KJ
authors.lastname: Clark
authors.forename: Anand
authors.initials: A
authors.lastname: Venkatraman
authors.forename: Jae-Woo
authors.initials: JW
authors.lastname: Kim
authors.forename: Robert D
authors.initials: RD
authors.lastname: Schnabel
authors.forename: C
authors.initials: C
authors.lastname: Michael Dickens
authors.forename: Russell D
authors.initials: RD
authors.lastname: Wolfinger
authors.forename: Scott C
authors.initials: SC
authors.lastname: Fahrenkrug
authors.forename: Jeremy F
authors.initials: JF
authors.lastname: Taylor
mesh_terms: D000818:Animals; D002417:Cattle; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D005796:Genes; D016678:Genome; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000737:chemistry*; D009928:Organ Specificity; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000737:chemistry*; D012680:Sensitivity and Specificity; D012815:Signal Processing, Computer-Assisted; D015398:Signal Transduction; D013552:Swine
chemical_list: D015345:Oligonucleotide Probes; D012333:RNA, Messenger