Gene expression and the concept of the phenotype

Studies in History and Philosophy of Science Part C :Studies in History and Philosophy of Biological and Biomedical Sciences

Volumn 38, Issue 1, 2007, Pages 238-254

  Nachtomy, Ohad ^a   Shavit, Ayelet ^b   Yakhini, Zohar ^c  

^a BAR ILAN UNIVERSITY   (Israel)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c AGILENT TECHNOLOGIES   (Israel)

Author keywords

Concept extension; Gene expression; Genotype; Phenotype

Indexed keywords

MESSENGER RNA;

ARTICLE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENETICS; GENOTYPE; HUMAN; MICROARRAY ANALYSIS; MOLECULAR BIOLOGY; MUTATION; NUCLEOTIDE SEQUENCE; PHENOTYPE;

BASE SEQUENCE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC RESEARCH; GENOTYPE; HUMANS; MICROARRAY ANALYSIS; MOLECULAR BIOLOGY; MUTATION; PHENOTYPE; RNA, MESSENGER; TRANSCRIPTION, GENETIC; VARIATION (GENETICS);

EID: 33847137716     PISSN: 13698486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.shpsc.2006.12.014     Document Type: Article

References (41)

1. Barrett, M. T., Scheffer A., Ben-Dor, A., Sampas, N., Lipson, D., Kincaid, R., Tsang, P., Curry, B., Baird, K., Meltzer, P. S., Yakhini, Z., Bruhn, L., & Laderman S. (2004). Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proceedings of the National Academy of Science, 101, 17765-17770.
2. Belmaker R.H. Medical progress: Bipolar disorder. The New England Journal of Medicine 351 (2004) 476-486
3. Berg P., and Singer M. Dealing with genes (1992), University of Science Books, Mill Valley, CA
4. Bergmann S., Ihmels J., and Barkai N. Similarities and differences in genome-wide expression data of six organisms. PLoS Biology 2 (2004) 85-92
5. Bhattacharjee, A., Richards, W. G., Staunton, J., Li, C., Monti, S., Vasa, P., Ladd, C., Beheshti, J., Bueno, R., Gillette, M., Loda, M., Weber, G., Mark, E. J., Lander, E. S., Wong, W., Johnson, B. E., Golub, T. R., Sugarbaker, D. J., & Meyerson, M. (2001). Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proceedings in the National Academy of Science USA, 98(24), 13790-13795.
6. Bignell, G. R., Huang, J., Greshock, J., Watt, S., Butler, A., West, S., Grigorova, M., Jones, K. W., Wei, W., Stratton M. R., Futreal, A. P., Weber, B., Shapero, M. H., & Wooster, R. (2004). High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Research, 14, 287-295.
7. Cheung V.G., and Spielman R.C. The genetics of variation in gene expression. Nature Genetics 32 (2002) 522-526
8. Cox N.J. Human genetics: An expression of interest. Nature 430 (2004) 733
9. Darvasi A. Genomics: Gene expression meets genetics. Nature 422 (2003) 269-290
10. Dunn L.C. A short history of genetics (1991), Iowa State University Press, Ames, IA
11. Falk R. What is a gene?. Studies in History and Philosophy of Science 17 (1986) 133-173
12. Flatt T. The evolutionary genetics of canalization. The Quarterly Review of Biology 80 (2005) 287-316
13. Gottesman I.I., and Gould T.D. The endophenotype concept in psychiatry: Etymology and strategic intentions. The American Journal of Psychiatry 160 (2003) 636-645
14. Habby J.L., and Lewontin R.C. A molecular approach to the hetrozygosity in natural populations. Genetics 54 (1966) 577-590
15. Harbison, C. T., Gordon, B., Lee, T. I., Rinaldi, N. I., Macisaac, K. D., Danford, T. W., Hannett, N. M., Tagne J. B., Reynolds, D. B., Yoo, J., Jennings, E. G., Zeitlinger, J., Pokholok, D. K., Kellis, M., Rolfe, A. P., Takusagawa, K. T., Lander, E. S., Gifford, D. K., Fraenkel, E., & Young R. A. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
16. Harman, O. S. (2006). History of classical genetics. In Encyclopedia of life sciences. http://www.els.net. Chichester: John Wiley & Sons, Ltd.
17. Harrington A. Re-enchanted science: Holism in German culture from Wilhelm II to Hitler (1996), Princeton University Press, Princeton
18. Harwood J. Styles of scientific thought (1993), The University of Chicago Press, Chicago
19. Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., Meltzer P., Gusterson, B., Esteller, M., Raffeld, M., Yakhini, Z., Ben-Dor A., Dougherty, E., Kononen, J., Bubendorf, L., Fehrle, W., Pittaluga, S., Gruvberger, S., Loman, N., Johannsson, O., Olsson, H., Wilfond, B., Sauter, G., Kallioniemi, O. P., Borg, A., & Trent, J. (2001). Gene expression profiles in hereditary breast cancer. The New England Journal of Medicine, 344, 539-548.
20. Johannsen W. Arvelighedslaerens elementer (1905), Gyldendalske Boghandel, Nordiske Forlag, København
21. Johannsen W. Elemente der exakten Erblichkeitslehre (1909), Gustav Fischer, Jena
22. Keller E.F. Refiguring life: Metaphors of twentieth century biology (1995), Columbia University Press, New York
23. Keller E.F. The century of the gene (2000), Harvard University Press, Cambridge, MA
24. Keller E.F. Making sense of life (2002), Harvard University Press, Cambridge, MA
25. Latour B. Science in action (1987), Harvard University Press, Cambridge, MA
26. Lewontin R.C. Genotype and phenotype. In: Keller E.F., and Lloyd E.A. (Eds). Keywords in evolutionary biology (1992), Harvard University Press, Cambridge, MA 137-144
27. Lewontin, R. C. (2004). The genotype/phenotype distinction. In E. N. Zalta (Ed.), The Stanford encyclopedia of philosophy. http://plato.stanford.edu. Stanford CA: Metaphysics Research Lab.
28. Mayr E. Towards a new philosophy of biology (1988), Harvard University Press, Cambridge, MA
29. Morgan T.H. The theory of the gene. The American Naturalist 51 (1917) 513-544
30. Morley, M., Molony, C. M., Weber, T. M., Devlin, J. L., Ewens, K. G., Spielman, R. S., & Cheung, V. G. (2004). Genetic analysis of genome-wide variation in human gene expression. Nature, 430, 743-747.
31. Moss L. What genes can't do (2002), MIT Press, Cambridge, MA
32. National Center for Biotechnology Information. (2004). Microarrays: Chipping away at the mysteries of science and medicine. In A science primer. http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html.
33. Rollow C.D. Phenotypes, their epigenetics, ecology and evolution (1995), Chapman and Hall, London
34. Schadt, E. E., Monks, S. A., Drake, T. A., Lusis, A. J., Che, N., Colinayo, V., Ruff, T. G., Milligan, S. B., Lamb, J. R., Cavet, G., Linsley, P. S., Mao, M., Stoughton, R. B., & Friend, S. H. (2003). Genetics of gene expression surveyed in maize, mouse and man. Nature, 422, 297-302.
35. Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D., & Futcher, B. (1988). Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell, 9, 3273-3297.
36. Stotz K., and Griffiths P. How scientists conceptualise genes: An empirical study. Studies in History and Philosophy of Biological and Biomedical Sciences 35 (2004) 647-673
37. Stuart J.M., Segal E., Koller D., and Kim S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 302 (2003) 249-255
38. Tsalenko, A., Sharan R., Kristensen V., Børessen-Dale, A.-L., Ben-Dor, A., & Yakhini, Z. (2005). Analysis of SNP-expression association matrices. In Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (pp. 135-143). Washington, DC: IEEE Computer Society.
39. Waters K.C. Genes made molecular. Philosophy of Science 61 (1994) 163-185
40. Weismann, A. (1889). The continuity of the germ-plasm as the foundation of a theory of heredity (E. Poulton, S. Schönland, & A. E. Shipley, Eds. & Trans.). In idem, Essays upon heredity and kindred biological problems (pp. 161-249). Oxford: Clarendon Press.
41. Wittgenstein, L. (1978). Remarks on the foundations of mathematics (3rd ed.) (G. H. von Wright, R. Rhees, & G. E. M. Anscombe, Eds.; G. E. M. Anscombe, Trans.). Oxford: Basil Blackwell.