Browse > Article
http://dx.doi.org/10.5187/JAST.2009.51.1.001

Functional Analysis of Expressed Sequence Tags from Hanwoo (Korean Cattle) cDNA Libraries  

Lim, Da-Jeong (National Institute of Animal Science, RDA)
Byun, Mi-Jeong (National Institute of Animal Science, RDA)
Cho, Yong-Min (National Institute of Animal Science, RDA)
Yoon, Du-Hak (National Institute of Animal Science, RDA)
Lee, Seung-Hwan (National Institute of Animal Science, RDA)
Shin, Youn-Hee (Insilicogen, Inc.)
Im, Seok-Ki (National Institute of Animal Science, RDA)
Publication Information
Journal of Animal Science and Technology / v.51, no.1, 2009 , pp. 1-8 More about this Journal
Abstract
We generated 57,598 expressed sequence tags (ESTs) from 3 cDNA libraries of Hanwooo (Korean Cattle), fat, loin, liver. Liver, intermuscular fat and longissimus dorsi tissues were obtained from a 24-month-old Hanwoo steer immediately after slaughter. cDNA library was constructed according to the oligocapped method. The EST data were clustered and assembled into unique sequences, 4,759 contigs and 7,587 singletons. To carry out functional analysis, Gene Ontology annotation and identification of significant leaf nodes were performed that were detected by searching significant p-values from $2^{nd}$ level GO terms to leaf nodes using Bonferroni correction. We found that 13, 26 and 8 significant leaf nodes are unique in the transcripts according to 3 GO categories, molecular function, biological process and cellular component. Also digital gene expression profiling using the Audic's test was performed and tissue specific genes were detected in the above 3 libraries.
Keywords
Hanwoo; EST; Gene Ontology; Audic's test;
Citations & Related Records
Times Cited By KSCI : 2  (Citation Analysis)
연도 인용수 순위
1 Vaananen, H. K., Takala, T. E., Tolonen, U., Vuori, J. and Myllyla, V. V. 1988. Muscle‐specific carbonic anhydrase III is a more sensitive marker of muscle damage than creatine kinase in neuromuscular disorders. Arch Neurol 45(11):1254-1256.   DOI   ScienceOn
2 Zadissa, A., McEwan, J. C. and Brown, C. M. 2007. Inference of transcriptional regulation using gene expression data from the bovine and human genomes. BMC Genomics 8:265.   DOI   ScienceOn
3 Zhong, S., Storch, K. F., Lipan, O., Kao, M. C., Weitz, C. J. and Wong, W. H. 2004. GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space. Applied bioinformatics 3(4):261-264.   DOI
4 Lee, S. H., Park, E. W., Cho, Y. M., Lee, J. W., Kim, H. Y., Lee, J. H., Oh, S. J., Cheong, I. C. and Yoon, D. H. 2006. Confirming single nucleotide polymorphisms from expressed sequence tag datasets derived from three cattle cDNA libraries. J Biochem Mol Biol 39(2):183-188.   DOI
5 Nafikov, R. A. and Beitz, D. C. 2007. Carbohydrate and lipid metabolism in farm animals. The Journal of nutrition 137(3):702-705.   DOI
6 Noh, S. J., Lee, K., Paik, H. and Hur, C. G. 2006. TISA: tissue-specific alternative splicing in human and mouse genes. DNA Res 13(5):229-243.   DOI
7 Sifre, L., Berge, P., Engel, E., Martin, J. F., Bonny, J. M., Listrat, A., Taylor, R. and Culioli, J. 2005. Influence of the spatial organization of the perimysium on beef tenderness. J Agric Food Chem 53(21):8390-8399.   DOI
8 Sonstegard, T. S. and van Tassell, C. P. 2004. Bovine genomics update : making a cow jump over the moon. Genet Res 84(1):3-9.   DOI   ScienceOn
9 Bonferroni, C. 1936. Teoria statistica delle classi e calcolo delle probabilit? Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali di Firenze 8:3-62.
10 Coulson, R. A. and Herbert, J. D. 1984. A role for carbonic anhydrase in intermediary metabolism. Ann N Y Acad Sci. 429:505-515.   DOI
11 Dvorak, C. M., Hyland, K. A., Machado, J. G., Zhang, Y., Fahrenkrug, S. C. and Murtaugh, M. P. 2005. Gene discovery and expression profiling in porcine Peyer’s patch. Veterinary immunology and immunopathology 105(3-4):301-315.   DOI   ScienceOn
12 Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome research 8(3):186-194.   DOI
13 Gordon, D., Abajian, C. and Green, P. 1998. Consed: a graphical tool for sequence finishing. Genome research 8(3):195-202.   DOI
14 Lee, S. H., Park, E. W., Cho, Y. M., Kim, S. K., Lee, J. H., Jeon, J. T., Lee, C. S., Im, S. K., Oh, S. J., Thompson, J. M. and Yoon, D. 2007. Identification of differentially expressed genes related to intramuscular fat development in the early and late fattening stages of hanwoo steers. J Biochem Mol Biol 40(5):757-764.   DOI
15 Hansen, C., Fu, A., Meng, Y., Okine, E., Hawken, R., Barris, W., Li, C. and Moore, S. S. 2004. Gene expression profiling of the bovine gastrointestinal tract. Genome 47(4):639-649.   DOI   ScienceOn
16 Hanson, R. W. and Ballard, F. J. 1967. The relative significance of acetate and glucose as precursors for lipid synthesis in liver and adipose tissue from ruminants. Biochem J 105(2):529-536.   DOI
17 Huang, X. and Madan, A. 1999. CAP3: A DNA sequence assembly program. Genome research 9(9):868-877.   DOI
18 Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 25(17):3389-3402.   DOI
19 Audic, S. and Claverie, J. M. 1997. The significance of digital gene expression profiles. Genome Res 7(10):986-995.   DOI
20 Baumann, R. G., Baldwin, R. L., t. Van Tassell, C. P., Sonstegard, T. S. and Matukumalli, L. K. 2005. Characterization of a normalized cDNA library from bovine intestinal muscle and epithelial tissues. Anim Biotechnol 16(1):17-29.   DOI   ScienceOn