Functional Analysis of Expressed Sequence Tags from Hanwoo (Korean Cattle) cDNA Libraries
2
조회
0
다운로드
3
인용
0
참고문헌
키워드
초록
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 2nd 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.
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 2nd 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.
참고문헌 (20)
- Altschul, S. F., "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic acids research, 25(17), pp.3389~3402 (1997)
- Audic, S, "The significance of digital gene expression profiles", Genome Res, 7(10), pp.986~995 (1997)
- Baumann, R. G, "Characterization of a normalized cDNA library from bovine intestinal muscle and epithelial tissues", Anim Biotechnol, 16(1), pp.17~29 (2005)
- Bonferroni, C, "Teoria statistica delle classi e calcolo delle probabilit?", pp.8(3)~8(62) (1936), Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali
- Coulson, R. A, "A role for carbonic anhydrase in intermediary metabolism", Ann N Y Acad Sci, 429, pp.505~515 (1984)
- Dvorak, C. M, "Gene discovery and expression profiling in porcine Peyer’s patch", Veterinary immunology and immunopathology, 105(3), pp.301~315 (2005)
- Ewing, B, "Base-calling of automated sequencer traces using phred. II. Error probabilities", Genome research, 8(3), pp.186~194 (1998)
- Gordon, D, "Consed: a graphical tool for sequence finishing", Genome research, 8(3), pp.195~202 (1998)
- Hansen, C, "Gene expression profiling of the bovine gastrointestinal tract", Genome, 47(4), pp.639~649 (2004)
- Hanson, R. W, "The relative significance of acetate and glucose as precursors for lipid synthesis in liver and adipose tissue from ruminants", Biochem J, 105(2), pp.529~536 (1967)
- Huang, X, "CAP3: A DNA sequence assembly program", Genome research, 9(9), pp.868~877 (1999)
- Duhak Yoon, "Identification of Differentially Expressed Genes Related to IntramuscularFat Development in the Early and Late Fattening Stages of Hanwoo Steers", BMB reports, 40(5), pp.757~764 (2007), 한국생화학분자생물학회
- 윤두학, "Confirming Single Nucleotide Polymorphisms from Expressed Sequence TagDatasets Derived from Three Cattle cDNA Libraries", BMB reports, 39(2), pp.183~188 (2006), 한국생화학분자생물학회
- Nafikov, R. A, "Carbohydrate and lipid metabolism in farm animals", The Journal of nutrition, 137(3), pp.702~705 (2007)
- Noh, S. J, "TISA: tissue-specific alternative splicing in human and mouse genes", DNA Res, 13(5), pp.229~243 (2006)
- Sifre, L, "Influence of the spatial organization of the perimysium on beef tenderness", J Agric Food Chem, 53(21), pp.8390~8399 (2005)
- Sonstegard, T. S, "Bovine genomics update: making a cow jump over the moon", Genet Res, 84(1), pp.3~9 (2004)
- Vaananen, H. K, "Muscle‐specific carbonic anhydrase III is a more sensitive marker of muscle damage than creatine kinase in neuromuscular disorders", Arch Neurol, 45(11), pp.1254~1256 (1988)
- Zadissa, A, "Inference of transcriptional regulation using gene expres- sion data from the bovine and human genomes", BMC Genomics, 8(265) (2007)
- Zhong, S, "GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space", Applied bioinformatics, 3(4), pp.261~264 (2004)