Submitted to: Veterinary Immunology and Immunopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/21/2005
Publication Date: 11/30/2005
Citation: Everts, R.E., Band, M.R., Liu, Z., Kumar, C.G., Liu, L., Loor, J.J., Oliveria, R., Lewin, H.A. 2005. A 7872 cNDA microarray and its use in bovine functional genomics. Veterinary Immunology and Immunopathology. 105:235-245
Interpretive Summary: Bovine cDNA microarray is among pioneers used for functional genomic studies on cattle in varied fields. At an invitation of Journal of Veterinary Immunology and Immunopathology, this article provided an updated gene annotation of the array with gene ontology terms. It reviewed several projects being conducted using this gene microarray. USDA scientist Dr. Liu led the Bovine cDNA microarray project and was responsible for array design and quality assessment of microarray fabrication, gene annotation, normalization, data analysis, and research project on transcription profiling of genetic merit for cattle before he joined USDA-ARS. This publication provides a tool reference and impacts functional genomic studies of bovine and for animal studies in general.
Technical Abstract: The strategy used to create and annotate a 7872 cNDA microarray from cattle placenta and spleen cDNA sequences is described. This microarray contains approximately 6,300 unique genes, as determined by BLASTIN and TBLASTX similarity search against the human and mouse UniGene and draft human genome sequence databases (build 34). Sequences on the array were annotated with gene ontology (GO) terms, thereby facilitating data analysis and interpretation. A total of 3,244 genes were annotated with GO terms. The array is rich in sequences encoding transcription factors, signal transducers, and cell cycle regulators. Current research being conducted with this array is described, and an overview of planned improvements in our microarray platform for cattle functional genomics is presented.