Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Exploring the new world of the genome with DNA microarrays

Abstract

Thousands of genes are being discovered for the first time by sequencing the genomes of model organisms, an exhilarating reminder that much of the natural world remains to be explored at the molecular level. DNA microarrays provide a natural vehicle for this exploration. The model organisms are the first for which comprehensive genome–wide surveys of gene expression patterns or function are possible. The results can be viewed as maps that reflect the order and logic of the genetic program, rather than the physical order of genes on chromosomes. Exploration of the genome using DNA microarrays and other genome–scale technologies should narrow the gap in our knowledge of gene function and molecular biology between the currently–favoured model organisms and other species.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Gene expression analysis using a DNA microarray.
Figure 2: A gene expression map of the yeast genome.
Figure 3: The yeast cell–cycle 'phaseogram'; gene expression during the yeast cell cycle.

References

  1. Goffeau, A. et al. Life with 6000 genes. Science 274, 563–567 (1996).

    Article  Google Scholar 

  2. Deloukas, P. et al. A physical map of 30,000 human genes. Science 282, 744–746 (1998).

    CAS  Article  Google Scholar 

  3. Bassett, D.E. Jr, Eisen, M.B. & Boguski, M.S. Gene expression informatics—it's all in your mine. Nature Genet. 21, 51– 55 (1999).

    CAS  Article  Google Scholar 

  4. Schena, M. et al. Quantitative monitoring of gene expression patterns with a cDNA microarray. Science 270, 467– 470 (1995).

    CAS  Article  Google Scholar 

  5. Shalon, D., Smith, S.J. & Brown, P.O. A DNA micro–array system for analyzing complex DNA samples using two–color fluorescent probe hybridization. Genome Res. 6, 639–645( 1996).

    CAS  Article  Google Scholar 

  6. Pease, A.C. et al. Light–generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl Acad. Sci. USA 91, 5022–5026 (1994).

    CAS  Article  Google Scholar 

  7. Lockhart, D.J. et al. Expression monitoring by hybridization to high–density oligonucleotide arrays. Nature Biotechnol. 14, 1675–1680 (1996).

    CAS  Article  Google Scholar 

  8. DeRisi, J.L., Iyer, V. & Brown, P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680– 686 (1997).

    CAS  Article  Google Scholar 

  9. Wodicka, L. et al. Genome–wide expression monitoring in Saccharomyces cerevisiae. Nature Biotechnol. 15, 1359 –1367 (1997).

    CAS  Article  Google Scholar 

  10. Lashkari, D.A. et al. Yeast genome microarrays for parallel genetic and gene expression analysis of the yeast genome. Proc. Natl Acad. Sci. USA 94, 13057–13062 (1997).

    CAS  Article  Google Scholar 

  11. Duggan, D.J., Bittner, M., Chen, Y., Meltzer, P. & Trent, J. Expression profiling using cDNA microarrays. Nature Genet. 21, 10–14 (1999).

    CAS  Article  Google Scholar 

  12. Cheung, V.G. et al. Making and reading microarrays. Nature Genet. 21, 15–19 (1999).

    CAS  Article  Google Scholar 

  13. Lipshutz, R.J., Fodor, S.P.A., Gingeras, T.R. & Lockhart, D.J. High density synthetic oligonucleotide arrays. Nature Genet. 21, 20–24 (1999).

    CAS  Article  Google Scholar 

  14. Shoemaker, D.D. et al. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar–coding strategy. Nature Genet. 14, 450–456 ( 1996).

    CAS  Article  Google Scholar 

  15. Cho, R.J. et al. Parallel analysis of genetic selections using whole genome oligonucleotide arrays. Proc. Natl Acad. Sci. USA 95, 3752 –3757 (1998).

    CAS  Article  Google Scholar 

  16. Nelson, S. et al. Genomic mismatch scanning: a new approach to genetic linkage mapping. Nature Genet. 4, 11– 18 (1993).

    CAS  Article  Google Scholar 

  17. Winzeler, E.A. et al. Direct allelic variation scanning of the yeast genome. Science 281, 1194–1197 ( 1998).

    CAS  Article  Google Scholar 

  18. Chu, S. et al. The transcriptional program of germ cell development in budding yeast. Science 282, 699– 705 (1998).

    CAS  Article  Google Scholar 

  19. Marton, M.J. et al. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nature Med. (in press).

  20. Cho, R.J. et al. A genome–wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. 2, 65– 73 (1998).

    CAS  Article  Google Scholar 

  21. Spellman, P.T. et al. Comprehensive identification of cell–cycle regulated genes in Saccharomyces cerevisiae. Mol. Biol. Cell. 95, 14863–14868 (1998).

    Google Scholar 

  22. Hauser, N.C. et al. Transcriptional profiling on all open reading frames of Saccharomyces cerevisiae. Yeast 14, 1209–1221 (1998).

    CAS  Article  Google Scholar 

  23. Eisen, M. et al. Cluster analysis and display of genome–wide expression patterns. Proc. Natl Acad. Sci. USA (in press).

  24. Cherry, J.M. et al. SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26, 73–79 ( 1998).

    CAS  Article  Google Scholar 

  25. Chervitz, S.A. et al. Comparing the complete protein sets of worm and yeast: orthology and divergence. Science (in press).

  26. Botstein, D. et al. Yeast as a model organism. Science 277, 1259–1260 (1998).

    Article  Google Scholar 

  27. Iyer, V.R. et al. The transcriptional program in the response of human fibroblasts to serum. Science (in press).

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Brown, P., Botstein, D. Exploring the new world of the genome with DNA microarrays. Nat Genet 21, 33–37 (1999). https://doi.org/10.1038/4462

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/4462

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing