Progress 10/01/02 to 09/30/07
Outputs
This project has continued to evolve from its initial objectives, and is thus being terminated. Instead of theoretical methods for improving thousands of genes, the focus has become practical methods for identifying which genes might be of interest for genetic improvement. This will have greater short-term impact. Progress this year has been in the use of microarray data to extract coexpression of genes. Coexpression implies joint regulation, in turn suggesting functional relationships. Methods being studied generate a correlation matrix among all genes from array expression data, then convert the matrix to a graph and use graph algorithms to find "cliques" of highly correlated genes. Statistical problems with these high-dimensional data (eg. 400 million correlations from 30 arrays) and with comparing cliques are of immediate interest.
Impacts
Methods are being developed to extract additional information from microarray experiments, focused on gene coexpression. This information will assist discovery of gene function, particularly how genes work together in networks. Identification of candidate genes for genetic improvement of livestock will then be easier, leading to a safe and plentiful food supply.
Publications
- Kim HY, Steward TP, Vyas KR, Saxton AM, Nishina PM, Naggert JK, Kim JH. 2005. Functional genomic study of dietary obesity in congenic mice. FASEB Journal 19 (5 Part 2 Suppl. S): A1498.
- Blouse GE, Peterson CB, Minor KH, Perron MJ, Saxton AM, Anagli JY, Shore JD. 2005. An ordered mechanism for assembly of complexes of vitronectin and plasminogen activator inhibitor-I: pre-steady state kinetic analysis of step-wise binding and conformational changes that trigger assembly. Thrombosis & Haemostasis 93 (4): A29.
- Peng, X, MA Langston, AM Saxton, N Baldwin, JR Snoddy. 2004. Detecting Network Motifs in Gene Co-expression Networks. Critical Assessment of Microarray Data Analysis V, Duke University, Nov 10-12, 2004.
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Progress 01/01/04 to 12/31/04
Outputs
Purpose of the project is to investigate how the extensive genomic data being collected might be used to increase rates of genetic improvement, by selecting on genotypes instead of phenotypes. Possibilities for converting this project from theoretical to practical application were explored this year, including SNP detection, microarray technology and QTL identification in various species (see publications). It is apparent that practical application is many years away. It will take extensive research to identify all genes in metabolic pathways, and estimate functional performance of those genes. Currently it is practical to genetically improve a population for a few genes (marker assisted selection), but the goal of this project is to improve hundreds of genes simultaneously. Theoretical work will continue.
Impacts
Potential impact of this research is to increase the rate of genetic improvement in agriculture. This would greatly assist efforts to produce a plentiful and safe food supply for the world.
Publications
- Wang, Y., Voy, B.J., Urs, S., Kim, S., Soltlani-Bejnood, M., Quigley, N., Heo, Y.-R., Standridge, M., Andersen, B., Dhar, M., Joshi, R., Wortman, P., Taylor, J.W., Chun, J., Leuze, M., Claycombe, K., Saxton, A.M. and Moustaid-Moussa, N. 2004. The human fatty acid synthase gene and de novo lipogenesis are coordinately regulated in human adipose tissue. J. Nutr. 134: 1032-1038.
- Urs, S., Smith, C., Campbell, B., Saxton, A.M., Taylor, J., Zhang, B., Snoddy, J.R., Jones Voy, B. and Moustaid-Moussa, N. 2004. Gene Expression Profiling in human preadipocytes and adipocytes by microarray analysis. J. Nutr. 134: 762-770.
- Panthee, D.R., Pantalone, V.R., Sams, C.E., Saxton, A.M., West, D.R. and Rayford. W.E. 2004. Genomic regions governing soybean seed nitrogen accumulation. J. Amer. Oil Chemists Soc. 81(1): 77-81.
- Youngerman, S.M., Saxton, A.M., Oliver, S.P. and Pighetti, G.M. 2004. Association of CXCR2 polymorphisms with subclinical and clinical mastitis in dairy cattle. J Dairy Science 87:2442-2448.
- Hyten, D.L., Pantalone, V.R., Sams, C.E., Saxton, A.M., Landau-Ellis, D., Stefaniak, T.R. and Schmidt, M.E. 2004. Seed quality QTL in a prominent soybean population. Theoretical and Applied Genetics 109(3): 552-561.
- Smiley, R.D., Saxton, A.M., Jackson, M.J., Hicks, S.N., Stinnett, L.G. and Howell, E.E. 2004. Non-Linear Fitting of Bi-Substrate Enzyme Kinetic Data using SAS: Application to R67 Dihydrofolate Reductase. Analytical Biochemistry 334(1): 204-206.
- Youngerman, S.M., Saxton, A.M. and Pighetti, G.M. 2004. Novel single nucleotide polymorphisms and haplotypes within the bovine CXCR2 gene. Immunogenetics 56(5): 355-359.
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