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6. References
Basten, C.J., Weir, B.S., and Zeng, Z.-B., 1994, Zmap—A QTL Cartographer, In Smith, C. et al., editor, In Proceedings of the 5th World Congress on Genetics Applied to Livestock Production: Computing Strategies and Software, volume 22, pages 65–66, Guelph, Ontario, Canada, 5th World Congress on Genetics Applied to Livestock Production, Organizing Committee.
Basten, C.J., Weir, B.S., and Zeng, Z.-B., 2002, QTL Cartographer, Department of Statistics, North Carolina University, Raleigh, NC, Version 1.16.
Black, M.A., and Doerge, R.W., 2002, Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments, Bioinformatics, 18:1609–1616.
Borevitz, J.O., Liang, D., Plouffe, D., Chang, H., Zhu, T., Weigel, D., Berry, C.C., Winzeler, E., and Chory, J., 2003, Large-scale identification of single-feature polymorphisms in complex genomes, Genome Research, 13:513–523.
Brem, R.B., Yvert, G., Clinton, R., and Kruglyak, L., 2002, Genetic dissection of transcriptional regulation in budding yeast, Science 296:752–755.
Broman, K.W., and Speed, T.P., 2002, A model selection approach for the identification of quantitative trait loci in experimental crosses, J. R. Statist. Soc. B, 64:641–656.
Chong, L., and Ray, L.B., 2002, Whole-istic biology, Science, 295:1661.
Churchill, G.A., 2002, Fundamentals of experimental design for cdna microarrays, Nature Genetics Supplement, 32:490–496.
Churchill, G.A., and Doerge, R.W., 1994, Empirical threshold values for quantitative trait mapping, Genetics, 138:963–971.
Cowles, C.R., Hirschhorn, J.N., Altshuler, D., and Lander, E.S., 2002, Detection of regulatory variation in mouse genes, Nature Genetics, 32:432–437.
Doerge, R.W., 2002, Mapping and analysis of quantitative trait loci in experimental populations, Nature Reviews Genetics, 3:43–52.
Duggan, D.J., Bittner, M., Chen, Y., Meltzer, P., and Trent, J.M., 1999, Expression profiling using cDNA microarrays, Nature Genetics Suppliment, 21:10–14.
Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D., 1998, Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. USA, 95:14863–14868.
Holter, N.S., Mitra, Maritan, A., Cieplak, M. Banavar, J.R., and Fedoroff, N.V., 2000, Fundamental patterns underlying gene expression profiles: simplicity from complexity, Proc. Natl. Acad. Sci. USA, 97:8409–8414.
Hughes, T., Marton, M., Jones, A., Roberts, C., Stoughton, R., Armour, C., Bennett, H., Dai, H., He, Y., Kidd, M., King, A., Meyer, M., Slade, D., Lum, P., Stepaniants, S., Shoemaker, D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M., and Friend, S., 2000, Functional discovery via a compendium of expression profile, Cell, 102:109–126.
Jang, W., Chen, H.C., Sicotte, H., and Schuler, G.D., 1999, Making effective use of human genomic sequence data, Trends in Genetics, 15:284–286.
Jansen, R.C., 2003, Studying complex biological systems using multifactorial perturbation, Nature Reviews Genetics, 4:145–151.
Jansen, R.C., and Nap, J.P., 2001, Genetical genomics: the added value from segregation, Trends in Genetics, 17:388–391.
Jiang, C., and Zeng, Z.-B., 1995, Multiple trait analysis of genetic mapping for quantitative trait loci, Genetics, 140:1111–1127.
Jin, W., Riley, R.M., Wolfinger, R.D., White, K.P., Passador-Gurgel, G., and Gibson, G., 2001, The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster, Nature Genetics, 29:389–395.
Kerr, M.K., and Churchill, G.A., 2001a, Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments, Proc. Natl. Acad. Sci. USA, 98:8961–8965.
Kerr, M.K., and Churchill, G.A., 2001b, Experimental design for gene expression microarrays, Biostatistics, 2:183–201.
Kerr, M.K., and Churchill, G.A., 2001c, Statistical design and the analysis of gene expression microarray data, Genet. Res., Camb., 77:123–128.
Kerr, M.K., Martin, M., and Churchill, G.A., 2000, Analysis of variance for gene expression microarray data, Journal of Computational Biology, 7:819–837.
Kitano, H., 2002, Systems biology: a brief overview, Science, 295:1662–1664.
Kodadek, T., 2001, Protein microarrays: prospects and problems, Chem. Biol., 8:105–115.
Lander, E.S., and Botstein, D., 1989, Mapping mendelian factors underlying quantitative traits using rflp linkage maps, Genetics, 121:185–199.
Lincoln, S.E., Daly, M.J., and Lander, E.S., 1992, Mapping Genes Controlling Quantative Traits with MAPMAKER/QTL, Whitehead Institute for Biomedical Research, Cambridge, MA 02142 USA, two edition, Version 1.1.
Lipshutz, R.J., Fodor, S.P.A., Gingeras, T.R., and Lockhart, D.J., 1999, High density synthetic oligonucleotide arrays, Nature Genetics Suppliment, 21:20–24.
MacBeath, G., 2002, Protein microarrays and proteomics, Nature Genetics Suppliment, 32:526–532.
Mackay, T.F., 2001, Quantitative trait loci in Drosophila, Nature Reviews Genetics, 2:11–20.
Mauricio, R., 2001, Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology, Nature Reviews Genetics, 2:370–381.
Mouse Genome Sequencing Consortium, 2002, Initial sequencing and comparative analysis of the mouse genome, Nature, 420:520–562.
Newton, M.A., Kendziorski, C.M., Richmond, C.S., Blattner, F.R., and Tsui, K.W., 2001, On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data, Journal of Computational Biology, 8:37–52.
Oleksiak, M.F., Churchill, G.A., and Crawford, D.L., 2002, Variation in gene expression within and among natural populations, Nature Genetics, 32:261–266.
Rossant, J., and Spence, A., 1998, Chimeras and mosaics in mouse mutant analysis, Trends in Genetics, 14:358–363.
Schadt, E.E., Monks, S.A., Drake, T.A., Lusis, A.J., Che, N., Collnayo, V., Ruff, T.G., Milligan, S.B., Lamb, J.R., Cavet, G., Linsley, P.S., Mao, M., Stoughton, R.B., and Friend, S.H., 2003, Genetics of gene expression surveyed in maize, mouse, and man, Nature, 422:297–302.
Schena, M., Shalon, D., Heller, R., Brown, A.C.P.O., and Davies, R.W., 1996, Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes, Proc. Natl. Acad. Sci. USA, 93:10614–10619.
Searle, S.R., 1971, Linear Models, John Wiley and Sons, Inc., New York, NY.
Service, R.F., 1999, Physics: The automated approach to protein structure, Science, 285:1345.
Steinmetz, L.M., Sinha, H., Richards, D.R., Spiegelman, J.I., Oefner, P.J., McCusker, J.H., and Davis, R.W., 2002, Dissecting the architecture of a quantitative trait locus in yeast, Nature, 416:326–330.
The Arabidopsis Genome Initiative, 2000, Analysis of the genome sequence of the flowering plant Arabidopsis Thaliana, Nature, 408:796–815.
Wayne, M.L., and McIntyre, L.M., 2002, Combining mapping and arraying: an approach to candidate gene identification, Proc. Natl. Acad. Sci. USA, 99:14903–14906.
Yan, H., Dobbie, Z., Gruber, S.B., Markowitz, S., Romans, K., Giardiello, F.M., Kinzler, K.W., and Vogelstein, B., 2002a, Small changes in expression affect predisposition to tumorigenesis, Nature Genetics, 30:25–26.
Yan, H., Yuan, W., Velculescu, V.E., Vogelstein, B., and Kinzler, K.W., 2002b, Allelic variation in human gene expression, Science, 297:1143.
Zeng, Z.-B., 1993, Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci, Proc. Natl. Acad. Sci. USA, 90:10972–10976.
Zeng, Z.-B., 1994, Precision mapping of quantitative trait loci, Genetics, 136:1457–1468.
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Kim, K., West, M.A.L., Michelmore, R.W., St. Clair, D.A., Doerge, R.W. (2005). Old Methods for New Ideas: Genetic Dissection of the Determinants of Gene Expression Levels. In: Gustafson, J.P., Shoemaker, R., Snape, J.W. (eds) Genome Exploitation. Springer, Boston, MA. https://doi.org/10.1007/0-387-24187-6_7
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