Lee et al. BMC Genomics 2010, 11:623 http://www.biomedcentral.com/1471-2164/11/623 Gene ontology (GO) analysis Annotation of DE probes was performed using the Database for Annotation. Visualization and Integrated Discovery (DAVID) http://david.abcc.ncifcrf.gov/home. jsp. In subsequent text the term “probe” is replaced by “gene”. The DE genes were analyzed in the context of their gene ontology (GO) biological process (Gene Ontology Consortium. 2006). Biological pathway analysis Differentially expressed genes in the m. longissimus of high and low marbled Hanwoo were clustered into pathways using the program Pathway studio (Stratagene, La Jolla, CA). This program provided a visual representation of the differentially expressed genes from the microarray data. In this study, 14 annotated genes out the 21 differentially expressed genes were imported into the program. Pathway studio then generated relationships between gene products using a literature search of curated genes and displayed the interactions in the form of pathways that can also include other genes/proteins, small molecules, cellular processes, and relevant transcription factors. If no interac- tions were found or proper annotation was not available, the gene was not included in the pathway. To help explicit the function of the genes in each pathway, gene ontology terms were determined for all genes illustrated within the pathways generated by Pathway studio 6.0. Acknowledgements This work was supported by awards from the International Collaborative research fund (Grant No: 200712A01032083) between the Rural Development Administration (RDA) in Korea and Cooperative Research Centre for Beef Genetic Technologies in Australia. Seung Hwan Lee held International Postgraduate Research Scholarship (IPRS) from University of New England (UNE). The authors also thank the anonymous reviewers for their helpful suggestions and comments. Author details 1Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Suwon 441-706, Korea. 2School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia. 3The Cooperative Research Centre for Beef Genetic Technologies, University of New England, Armidale, NSW 2351, Australia. 4The Centre for Genetic Analysis and Applications, University of New England, Armidale, NSW 2351, Australia. Authors’ contributions S.H.L and C.G were involved in designing and planning of the study. They carried out the experiments and analyses, interpreted data, annotation and statistical analyses and wrote the first draft of the paper. N.K.K and D.L were involved in the realtime PCR analysis, pathway analysis and contributed to the writing of the paper. 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