Functional genomic technologies: Creating new paradigms for fundamental and applied biology

Biotechnology Progress

Volumn 15, Issue 3, 1999, Pages 304-311

  Kao, Camilla M ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOENGINEERING; BIOLOGICAL FUNCTIONS; GENOME ANALYSIS;

BIOTECHNOLOGY; DNA SEQUENCES; ENGINEERING RESEARCH; GENES; MATHEMATICAL MODELS; METABOLITES;

APPLIED BIOLOGY; FUNCTIONAL GENOMIC TECHNOLOGY; SECONDARY METABOLITE PRODUCTION;

GENETIC ENGINEERING;

BIOTECHNOLOGY; DNA; GENE EXPRESSION; GENOME; GENOME, FUNGAL; SACCHAROMYCES CEREVISIAE;

EID: 0033136114     PISSN: 87567938     EISSN: None     Source Type: Journal    
DOI: 10.1021/bp990027q     Document Type: Article

References (43)

1. Brown, P. O.; Botstein, D. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 1999, 21, 33-37; http://library.genetics.nature.com/server-java/Propub/ genetics/ng0199supp.contents (publicly available online).
2. Nat. Gene. Suppl. 1999, 21; http://library.genetics.nature. com/server-java/Propub/genetics/ng0199supp.contents (publicly available online).
3. Eisen, M. B.; Brown, P. O. DNA arrays for analysis of gene expression, Methods Enzymol. 1999, in press.
4. DeRisi, J.; Iyer, V. Curr. Opin. Oncol. 1999, 11, 76-79.
5. Alizadeh, A.; Eisen, M.; Botstein, D.; Brown, P. O.; Staudt, L. M. Probing lymphocyte biology by genomic-scale gene expression analysis, J. Clin. Immunol. 1998, 18, 373-379.
6. Goffeau, A.; Barrell, B. G.; Bussey, H.; Davis, R. W.; Dujon, B.; Feldmann, H.; Galibert, F.; Hoheisel, J. D.; Jacq, C.; Johnston, M.; Louis, E. J.; Mewes, H. W.; Murakami, Y.; Philippsen, P.; Tettelin, H.; Oliver, S. G. Life with 6000 genes. Science 1996, 274, 546-567.
7. Blattner, F. R.; Plunkett, G. I.; Bloch, C. A.; Perna, N. T.; Burland, V.; Riley, M.; Collado-Vides, J.; Glasner, J. D.; Rode, C. K.; Mayhew, G. F.; Gregor, J.; Davis, N. W.; Kirkpatrick, H. A.; Goeden, M. A.; Rose, D. J.; Mau, B.; Shao, Y. The complete genome sequence of Escherichia coli K-12. Science 1997, 277, 1453-1474.
8. Smith, V.; Botstein, D.; Brown, P. O. Genetic footprinting: A genomic strategy for determining a gene's function given its sequence. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 6479-6483.
9. Smith, V.; Chou, K. N.; Lashkari, D.; Botstein, D.; Brown, P. O. Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science 1996, 274, 2069-2074.
10. Dunn, B.; Metzner, S.; Chung, E.; Ferea, T.; Botstein, D.; Brown, P. O. personal communication.
11. http://sequence-www.stanford.edu/group/yeast_deletion_ project/deletion.html.
12. Shoemaker, D. D.; Lashkari, D. A.; Morris, D.; Mittmann, M.; Davis, R. W. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat. Genet. 1996, 14, 450-456.
13. Ross-Macdonald, P.; Sheehan, A.; Roeder, G. S.; Snyder, M. A multipurpose transposon system for analyzing protein production, localization, and function in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 190-195.
14. http://ycmi.med.yale.edu/YGAC/home.html.
15. McAllister, L.; Penland, L.; Brown, P. O. Enrichment for loci identical-by-descent between pairs of mouse or human genomes by genomic mismatch scanning. Genomics 1998, 47, 7-11.
16. Winzeler, E. A.; Richards, D. R.; Conway, A. R.; Goldstein, A. L.; Kalman, S.; McCullough, M. J.; McCusker, J. H.; Stevens, D. A.; Wodicka, L.; Lockhart, D. J.; Davis, R. W. Direct allelic variation scanning of the yeast genome. Science 1998, 281, 1194-1197.
17. Wang, D. G.; Fan, J. B.; Siao, C. J.; Berno, A.; Young, P.; Sapolsky, R.; Ghandour, G.; et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 1998, 280, 1077-1082.
18. Pollack, J.; Perou, C.; Jeffrey, S.; Botstein, D.; Brown, P. O. Microarray analysis of DNA copy number changes in cancer. Manuscript in preparation.
19. Velculescu, V. E.; Zhang, L.; Zhou, W.; Vogelstein, J.; Basrai, M. A.; Bassett, D. E. J.; Hieter, P.; Vogelstein, B.; Kinzler, K. W. Characterization of the yeast transcriptome. Cell 1997, 88, 243-251.
20. Chee, M.; Yang, R.; Hubbell, E.; Berno, A.; Huang, X. C.; Stern, D.; Winkler, J.; Lockhart, D. J.; Morris, M. S.; Fodor, S. P. Accessing genetic information with high-density DNA arrays. Science 1996, 274, 610-614.
21. Lockhart, D. J.; Dong, H.; Byrne, M. C.; Follettie, M. T.; Gallo, M. V.; Chee, M. S.; Mittmann, M.; Wang, C.; Kobayashi, M.; Horton, H.; Brown, E. L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 1996, 14, 1675-1680.
22. Wodicka, L.; Dong, H.; Mittmann, M.; Ho, M. H.; Lockhart, D. J. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 1997, 15, 1359-1367.
23. http://www.affymetrix.com/.
24. Schena, M.; Shalon, D.; David, R. W.; Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270, 467-470.
25. Shalon, D.; Smith, S. J.; Brown, P. O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 1996, 6, 639-645.
26. Lashkari, D. A.; DeRisi, J. L.; McCusker, J. H.; Namath, A. F.; Gentile, C.; Hwang, S. Y.; Brown, P. O.; Davis, R. W. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 13057-13062.
27. http://www.incyte.com/products/arrays/index.html.
28. http://cmgm.stanford.edu/pbrown/mguide/index.html.
29. For a standard reverse transcription reaction, ∼2 μg mRNA is required. However, an RNA amplification protocol has been developed to amplify samples as small as ∼20 ng mRNA (30).
30. Barry, C. T.; Botstein, D.; Brown, P. O. Characterization of an RNA amplification procedure as applied to cDNA microarray analysis. Manuscript in preparation.
31. O'Hagan, D. The polyketide metabolites 1-176; E. Horwood: New York, 1991.
32. http://www.sanger.ac.uk/Projects/S_coelicolor/.
33. Iyer, V. R.; Eisen, M. B.; Ross, D. T.; Schuler, G.; Moore, T.; Lee, J. C. F.; Trent, J. M.; Staudt, L. M.; Hudson, J. J.; Boguski, M. S.; Lashkari, D.; Shalon, D.; Botstein, D.; Brown, P. O. The transcriptional program in the response of human fibroblasts to serum. Science 1999, 283, 83-87; http:// genome-www.stanford.edu/serum/.
34. Spellman, P. T.; Sherlock, G.; Zhang, M. Q.; Iyer, V. R.; Anders, K.; Eisen, M. B.; Brown, P. O.; Botstein, D.; Futcher, B. Comprehensive identification of cell cycle regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 1998, 9, 3273-3297; http:// genome-www.stanford.edu/cellcycle/.
35. Chu, S.; DeRisi, J.; Eisen, M.; Mulholland, J.; Botstein, D.; Brown, P. O.; Herskowitz, I. The transcriptional program of sporulation in budding yeast, Science 1998, 282, 699-705; http://cmgm.stanford.edu/pbrown/sporulation/.
36. DeRisi, J. L.; Iyer, V. R.; Brown, P. O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278, 680-686; http://cmgm.stanford.edu/ pbrown/explore/.
37. Ross, D. T.; Scherf, U.; Perou, C.; Eisen, M. B.; Weinstein, J.; Botstein, D.; Brown, P. O. Gene expression patterns in the NCI60 human tumor-derived cell lines. Manuscript in preparation.
38. Perou, C. M.; Jeffrey, S. S.; van de Rijn, M.; Eisen, M. B.; Ross, D. T.; Pergamenschikov, A.; Williams, C.; Zhu, S. X.; Lee, J. C. F.; Lashkari, D.; Shalon, D.; Brown, P. O.; Botstein, D. Identification of distinctive gene expression profiles in human breast epithelial cells. Manuscript in preparation.
39. Gasch, A.; Botstein, D.; Brown, P. O. Gene expression patterns of S. cerevisiae in response to oxidative stress using DNA microarrays. Manuscript in preparation.
40. Kao, C. M.; Botstein, D.; Brown, P. O. Gene expression analysis of stationary phase and starvation in S. cerevisiae. Manuscript in preparation.
41. Eisen, M. B.; Spellman, P. T.; Brown, P. O.; Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 14863-14868; http://rana.stanford.edu/clustering/.
42. http://www.sdsc.edu/meme/meme/website/.
43. http://alize.ulb.ac.be/∼YRT.