Functional annotation of genomic data with metabolic inference

Poultry Science

Volumn 86, Issue 7, 2007, Pages 1510-1522

  Walzem, R L ^a   Baillie, R A ^b   Wiest, M ^b   Davis, R ^b   Watkins, S M ^b   Porter, T E ^c   Simon, J ^d   Cogburn, L A ^e  

^a TEXAS A AND M UNIVERSITY   (United States)

^b Lipomics Technologies   (United States)

^c UNIVERSITY OF MARYLAND   (United States)

^d STATION DE RECHERCHES AVICOLES   (France)

^e UNIVERSITY OF DELAWARE   (United States)

Author keywords

Adipose; Chicken lipid; Genetic selection; Metabolomics

Indexed keywords

GALLUS GALLUS;

ANIMAL; ARTICLE; BODY WEIGHT; CHICKEN; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC SELECTION; GENETICS; GENOMICS; LIPID METABOLISM; MALE; METABOLISM; SYSTEMS BIOLOGY;

ANIMALS; BODY WEIGHT; CHICKENS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOMICS; LIPID METABOLISM; MALE; SELECTION (GENETICS); SYSTEMS BIOLOGY;

EID: 34548286913     PISSN: 00325791     EISSN: 15253171     Source Type: Journal    
DOI: 10.1093/ps/86.7.1510     Document Type: Conference Paper

References (66)

1. Ametaj, B. N., D. G. V. Emmanuel, M. J. Lewis, K. Jeroncic, L. Nikolai, S. Shanthipoosan, and D. S. Wishart. 2006. Bovine metabolomics: Profiling of rumen fluid metabolites in dairy cattle. Proc. Sec. Annu. Metabolomics Symp., Timms Cent., Univ. Alberta, Edmonton, Canada.
2. Assaf, S., S. Lagarrigue, S. Daval, M. Sansom, B. Leclercq, J. Michel, F. Pitel, M. Alizadeh, A. Vignal, and M. Douaire. 2004. Genetic linkage and expression analysis of SREBP and lipogenic genes in fat and lean chicken. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 137:433-441.
3. Biggs, H. G., and L. Edwards. 1975. A manual colorimetric assay of triglycerides in serum. Clin. Chem. 21:437-441.
4. Bourneuf, E., F. Herault, C. Chicault, W. Carre, S. Assaf, A. Monnier, S. Mottier, S. Lagarrigue, M. Douaire, J. Mosser, and C. Diot. 2006. Microarray analysis of differential gene expression in the liver of lean and fat chickens. Gene 372:162-170.
5. Brown, A., D. Wiggins, and G. F. Gibbons. 1999. Manipulation of cholesterol and cholesteryl ester synthesis has multiple effects on the metabolism of apolipoprotein B and the secretion of very-low-density lipoprotein by primary hepatocyte cultures. Biochim. Biophys. Acta 1440:253-265.
6. Burns, M. A., W. He, C. L. Wu, and L. L. Cheng. 2004. Quantitative pathology in tissue MR spectroscopy based human prostate metabolomics. Technol. Cancer Res. Treat. 3:591-598.
7. Buyse, J., F. R. Leenstra, M. Zeman, G. Rahimi, and E. Decuypere. 1999. A comparative study of different selection strategies to breed leaner meat-type poultry. Poult. Avian Biol. Rev. 10:121-142.
8. Carre, W., X. Wang, T. E. Porter, Y. Nys, J. Tang, E. Bernberg, R. Morgan, J. Burnside, S. E. Aggrey, J. Simon, and L. A. Cogburn. 2006. Chicken genomics resource: Sequencing and annotation of 35,407 ESTs from single and multiple tissue cDNA libraries and CAP3 assembly of a chicken gene index. Physiol. Genomics 25:514-524.
9. Castle, A. L., O. Fiehn, R. Kaddurah-Daouk, and J. C. Lindon. 2006. Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results. Brief. Bioinform. 7:159-165.
10. Chen, S. E., J. P. McMurtry, and R. L. Walzem. 2006. Overfeeding-induced ovarian dysfunction in broiler breeder hens is associated with lipotoxicity. Poult. Sci. 85:70-81.
11. Cogburn, L. A., X. Wang, W. Carré, L. Rejto, S. E. Aggrey, M. J. Duclos, J. Simon, and T. E. Porter. 2004. Functional genomics in chickens: Developement of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways. Comp. Funct. Genomics 2:253-261.
12. Cogburn, L. A., X. Wang, W. Carre, L. Rejto, T. E. Porter, S. E. Aggrey, and J. Simon. 2003. Systems-wide chicken DNA microarrays, gene expression profiling, and discovery of functional genes. Poult. Sci. 82:939-951.
13. Cotter, D., A. Maer, C. Guda, B. Saunders, and S. Subramaniam. 2006. LMPD: LIPID MAPS proteome database. Nucleic Acids Res. 34:D507-D510.
14. Csete, M. E., and J. C. Doyle. 2002. Reverse engineering of biological complexity. Science 295:1664-1669.
15. Dixon, R. A., D. R. Gang, A. J. Charlton, O. Fiehn, H. A. Kuiper, T. L. Reynolds, R. S. Tjeerdema, E. H. Jeffery, J. B. German, W. P. Ridley, and J. N. Seiber. 2006. Applications of metabolomics in agriculture. J. Agric. Food Chem. 54:8984-8994.
16. Drackley, J. K., S. S. Donkin, and C. K. Reynolds. 2006. Major advances in fundamental dairy cattle nutrition. J. Dairy Sci. 89:1324-1336.
17. Fiehn, O. 2002. Metabolomics-the link between genotypes and phenotypes. Plant Mol. Biol. 48:155-171.
18. Folch, J., M. Lee, and G. H. Sloane-Stanley. 1957. A simple method for the isolation and purification of total lipids from animal tissues. J. Biol. Chem. 226:497-509.
19. German, J. B., L. A. Gillies, J. T. Smilowitz, A. M. Zivkovic, and S. M. Watkins. 2007. Lipidomics and lipid profiling in metabolomics. Curr. Opin. Lipidol. 18:66-71.
20. Golub, T. R., D. K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J. P. Mesirov, H. Coller, M. L. Loh, J. R. Downing, M. A. Caligiuri, C. D. Bloomfield, and E. S. Lander. 1999. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286:531-537.
21. Griffin, J. L., and M. E. Bollard. 2004. Metabonomics: Its potential as a tool in toxicology for safety assessment and data integration. Curr. Drug Metab. 5:389-398.
22. Griffin, J. L., C. K. Cemal, and M. A. Pook. 2004. Defining a metabolic phenotype in the brain of a transgenic mouse model of spinocerebellar ataxia 3. Physiol. Genomics 16:334-340.
23. Griffin, H. D., and C. Goddard. 1994. Rapidly growing broiler (meat-type) chickens: Their origin and use for comparative studies of the regulation of growth. Int. J. Biochem. 26:19-28.
24. Gurr, M. I., J. L. Harwood, and K. N. Frayn. 2002. Lipid Biochemistry: An Introduction. Blackwell Science, Oxford, UK.
25. Hermier, D., and M. J. Chapman. 1985. Plasma lipoproteins and fattening: Description of a model in the domestic chicken, Gallus domesticus. Reprod. Nutr. Dev. 25:235-241.
26. Hermier, D., M. J. Chapman, and B. Leclercq. 1984. Plasma lipoprotein profile in fasted and refed chickens of two strains selected for high or low adiposity. J. Nutr. 114:1112-1121.
27. Hermier, D., P. Forgez, and M. J. Chapman. 1985. A density gradient study of the lipoprotein and apolipoprotein distribution in the chicken, Gallus domesticus. Biochim. Biophys. Acta 836:105-118.
28. Julian, R. J. 2005. Production and growth related disorders and other metabolic diseases of poultry-a review. Vet. J. 169:350-369.
29. Kitano, H. 2002. Systems biology: A brief overview. Science 295:1662-1664.
30. Lane, G. 2006. Urinary biomakers of forage feeding from ESIMS/ MS fingerprinting: Exploratory studies. N. Z. Soc. Anim. Prod. 66:230-235.
31. Leclercq, B. 1988. Genetic selection of meat-type chickens for high or low abdominal fat. Pages 25-40 in Leanness in Domestic Birds: Genetic, Metabolic and Hormonal Aspects. B. Leclercq and C. C. Whitehead, ed. Butterworths, London, UK.
32. Leclercq, B., J. C. Blum, and J. P. Boyer. 1980. Selecting broilers for low and high abdominal fat: Initial observations. Br. Poult. Sci. 21:107-113.
33. Leclercq, B., B. Chevalier, M. Derouet, and J. Simon. 1988. In vitro sensitivity of adipocytes from lean or fat chickens to glucagon and an analogue of adenosine. Pages 239-242 in Leanness in Domestic Birds: Genetic, Metabolic and Hormonal Aspects. B. Leclercq and C. C. Whitehead, ed. Butterworths, London, UK.
34. Leclercq, B., D. Hermier, and G. Guy. 1990. Metabolism of very low density lipoproteins in genetically lean or fat lines of chicken. Reprod. Nutr. Dev. 30:701-715.
35. Leclercq, B., D. Hermier, and M. R. Salichon. 1984. Effects of age and diet on plasma lipid and glucose concentrations in genetically lean or fat chickens. Reprod. Nutr. Dev. 24:53-61.
36. Legrand, P., and D. Hermier. 1992. Hepatic Δ9 desaturation and plasma VLDL level in genetically lean and fat chickens. Int. J. Obes. Relat. Metab. Disord. 16:289-294.
37. Liang, J. J., P. Oelkers, C. Guo, P. C. Chu, J. L. Dixon, H. N. Ginsberg, and S. L. Sturley. 2004. Overexpression of human diacylglycerol acyltransferase 1, acyl-coa:cholesterol acyltransferase 1, or acyl-CoA:cholesterol acyltransferase 2 stimulates secretion of apolipoprotein B-containing lipoproteins in McA-RH7777 cells. J. Biol. Chem. 279:44938-44944.
38. Mayes, P. A. 2000. Metabolism of acylglycerols and sphingolipids. Pages 259-267 in Harper's Review of Biochemistry. R. K. Murray, P. A. Mayes, and V. W. Rodwell, ed. Appleton and Lange, Stamford, CT.
39. Mehrotra, B., and P. Mendes. 2006. Bioinformatics approaches to integrate metabolomics and other systems biology data. Pages 105-115 in Biotechnology in Agricultrure and Forestry. K. Saito, R. A. Dixon, and L. Willmitzer, ed. Springer-Verlag, Berlin, Germany.
40. Moran, F. M., A. G. Hendrickx, S. Shideler, J. W. Overstreet, S. M. Watkins, and B. L. Lasley. 2004. Effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on fatty acid availability and neural tube formation in cynomolgus macaque, Macaca fascicularis. Birth Defects Res. Part B Dev. Reprod. Toxicol. 71:37-46.
41. Morris, M., and S. M. Watkins. 2005. Focused metabolomic profiling in the drug development process: Advances from lipid profiling. Curr. Opin. Chem. Biol. 9:407-412.
42. Ohta, A., M. C. Mayo, N. Kramer, and W. E. Lands. 1990. Rapid analysis of fatty acids in plasma lipids. Lipids 25:742-747.
43. Ricard, F. H. 1975. A trial of selecting chickens on their growth curve pattern: Experimental design and first general results. Ann. Genet. Sel. Anim. 7:427-443.
44. Saadoun, A., and B. Leclercq. 1986. In vivo lipogenesis in genetically fat and lean chickens of various ages. Comp. Biochem. Physiol. B 83:607-611.
45. Saltzman, E., H. I. Katcher, P. J. Gillies, P. M. Kris-Etherton, J. Wylie-Rosett, F. Vinicor, B. Dawson-Hughes, Y.-I. Kim, C. L. Baum, C. McIssac, T. Masud, W. E. Mitch, C. J. Mclain, D. B. Hill, L. Marsano, H. McGuire, and J. D. Ard. 2006. Nutrition and Chronic Diseases in Present Knowledge in Nutrition. Vol. II. B. A. Bowman and R. M. Russell, ed. Int. Life Sci. Inst., Washington, DC.
46. Schilling, C. H., S. Schuster, B. O. Palsson, and R. Heinrich. 1999. Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15:296-303.
47. Simon, J., S. Guillaumin, B. Chevalier, M. Derouet, G. Guy, G. Marche, F. H. Ricard, and B. Leclercq. 2000. Plasma glucose-insulin relationship in chicken lines selected for high or low fasting glycaemia. Br. Poult. Sci. 41:424-429.
48. Skiba-Cassy, S., A. Collin, P. Chartrin, F. Medale, J. Simon, M. J. Duclos, and S. Tesseraud. 2007. Chicken liver and muscle carnitine palmitoyltransferase 1: Nutritional regulation of messengers. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 147:278-287.
49. Stone, S. J., H. M. Myers, S. M. Watkins, B. E. Brown, K. R. Feingold, P. M. Elias, and R. V. Farese Jr. 2004. Lipopenia and skin barrier abnormalities in DGAT2-deficient mice. J. Biol. Chem. 279:11767-11776.
50. Sysi-Aho, M., M. Katajamaa, L. Yetukuri, and M. Oresic. 2007. Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformatics 8:93. (Abstr.)
51. Team, R. D. C. 2005. R:ALanguage and Environment for Statistical Computing. R. Found. Stat. Comput., Vienna, Austria.
52. Thomas, C. E., and G. Ganji. 2006. Integration of genomic and metabonomic data in systems biology-are we 'there' yet? Curr. Opin. Drug Discov. Devel. 9:92-100.
53. Trethewey, R. N. 2001. Gene discovery via metabolic profiling. Curr. Opin. Biotechnol. 12:135-138.
54. Tsai, J., W. Qiu, R. Kohen-Avramoglu, and K. Adeli. 2007. MEKERK inhibition corrects the defect in VLDL assembly in HepG2 cells: Potential role of ERK in VLDL-ApoB100 particle assembly. Arterioscler. Thromb. Vasc. Biol. 27:211-218.
55. Vance, D. E. 1991. Phospholipid metabolism and cell signalling in eucaryotes. Pages 205-240 in Biochemistry of Lipids, Lipoproteins and Membranes. Vol. 20. D. E. Vance and J. Vance, ed. Elsevier, Amsterdam, the Netherlands.
56. Verhoeckx, K. C., S. Bijlsma, S. Jespersen, R. Ramaker, E. R. Verheij, R. F. Witkamp, J. van der Greef, and R. J. Rodenburg. 2004. Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and metabolomics in combination with multivariate data analysis. Int. Immunopharmacol. 4:1499-1514.
57. Walzem, R. L. 1996. Lipoproteins and the laying hen: Form follows function. Poult. Avian Biol. Rev. 7:31-64.
58. Walzem, R. L., S. Watkins, E. N. Frankel, R. J. Hansen, and J. B. German. 1995. Older plasma lipoproteins are more susceptible to oxidation: A linking mechanism for the lipid and oxidation theories of atherosclerotic cardiovascular disease. Proc. Natl. Acad. Sci. USA 92:7460-7464.
59. Watkins, S. M. 2000. Comprehensive lipid analysis: A powerful netanomic tool for predictive and diagnostic medicine. Isr. Med. Assoc. J. 2:722-724.
60. Watkins, S. M., B. D. Hammock, J. W. Newman, and J. B. German. 2001a. Individual metabolism should guide agriculture toward foods for improved health and nutrition. Am. J. Clin. Nutr. 74:283-286.
61. Watkins, S. M., T. Y. Lin, R. M. Davis, J. R. Ching, E. J. DePeters, G. M. Halpern, R. L. Walzem, and J. B. German. 2001b. Unique phospholipid metabolism in mouse heart in response to dietary docosahexaenoic or α-linolenic acids. Lipids 36:247-254.
62. Watkins, S. M., P. R. Reifsnyder, H. J. Pan, J. B. German, and E. H. Leiter. 2002. Lipid metabolome-wide effects of the PPARγ agonist rosiglitazone. J. Lipid Res. 43:1809-1817.
63. Watkins, S. M., X. Zhu, and S. H. Zeisel. 2003. Phosphatidylethanolamine- N-methyltransferase activity and dietary choline regulate liver-plasma lipid flux and essential fatty acid metabolism in mice. J. Nutr. 133:3386-3391.
64. Wiest, M. M., and S. M. Watkins. 2007. Biomarker discovery using high-dimensional lipid analysis. Curr. Opin. Lipidol. 18:181-186.
65. Xu, J., A. B. Keeton, J. L. Franklin, X. Li, D. Y. Venable, S. J. Frank, and J. L. Messina. 2006. Insulin enhances growth hormone induction of the MEK/ERK signaling pathway. J. Biol. Chem. 281:982-992.
66. Zhang, S., H. Li, and H. Shi. 2006. Single marker and haplotype analysis of the chicken apolipoprotein B gene T123G and D9500D9-polymorphism reveals association with body growth and obesity. Poult. Sci. 85:178-184.