Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1996 Oct 1;93(20):10614–10619. doi: 10.1073/pnas.93.20.10614

Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.

M Schena 1, D Shalon 1, R Heller 1, A Chai 1, P O Brown 1, R W Davis 1
PMCID: PMC38202  PMID: 8855227

Abstract

Microarrays containing 1046 human cDNAs of unknown sequence were printed on glass with high-speed robotics. These 1.0-cm2 DNA "chips" were used to quantitatively monitor differential expression of the cognate human genes using a highly sensitive two-color hybridization assay. Array elements that displayed differential expression patterns under given experimental conditions were characterized by sequencing. The identification of known and novel heat shock and phorbol ester-regulated genes in human T cells demonstrates the sensitivity of the assay. Parallel gene analysis with microarrays provides a rapid and efficient method for large-scale human gene discovery.

Full text

PDF
10614

Images in this article

10615Fig. 1
on p.10615
10616Fig. 2
on p.10616
10618Fig. 3
on p.10618

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adams M. D., Kelley J. M., Gocayne J. D., Dubnick M., Polymeropoulos M. H., Xiao H., Merril C. R., Wu A., Olde B., Moreno R. F. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991 Jun 21;252(5013):1651–1656. doi: 10.1126/science.2047873. [DOI] [PubMed] [Google Scholar]
  2. Adams M. D. Serial analysis of gene expression: ESTs get smaller. Bioessays. 1996 Apr;18(4):261–262. doi: 10.1002/bies.950180402. [DOI] [PubMed] [Google Scholar]
  3. Baeuerle P. A., Henkel T. Function and activation of NF-kappa B in the immune system. Annu Rev Immunol. 1994;12:141–179. doi: 10.1146/annurev.iy.12.040194.001041. [DOI] [PubMed] [Google Scholar]
  4. Becker J., Craig E. A. Heat-shock proteins as molecular chaperones. Eur J Biochem. 1994 Jan 15;219(1-2):11–23. doi: 10.1007/978-3-642-79502-2_2. [DOI] [PubMed] [Google Scholar]
  5. Bernard K., Auphan N., Granjeaud S., Victorero G., Schmitt-Verhulst A. M., Jordan B. R., Nguyen C. Multiplex messenger assay: simultaneous, quantitative measurement of expression of many genes in the context of T cell activation. Nucleic Acids Res. 1996 Apr 15;24(8):1435–1442. doi: 10.1093/nar/24.8.1435. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chan A. C., Desai D. M., Weiss A. The role of protein tyrosine kinases and protein tyrosine phosphatases in T cell antigen receptor signal transduction. Annu Rev Immunol. 1994;12:555–592. doi: 10.1146/annurev.iy.12.040194.003011. [DOI] [PubMed] [Google Scholar]
  7. Cohen G. B., Ren R., Baltimore D. Modular binding domains in signal transduction proteins. Cell. 1995 Jan 27;80(2):237–248. doi: 10.1016/0092-8674(95)90406-9. [DOI] [PubMed] [Google Scholar]
  8. Collins F. S. Ahead of schedule and under budget: the Genome Project passes its fifth birthday. Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):10821–10823. doi: 10.1073/pnas.92.24.10821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Crabtree G. R., Clipstone N. A. Signal transmission between the plasma membrane and nucleus of T lymphocytes. Annu Rev Biochem. 1994;63:1045–1083. doi: 10.1146/annurev.bi.63.070194.005145. [DOI] [PubMed] [Google Scholar]
  10. Craig E. A., Weissman J. S., Horwich A. L. Heat shock proteins and molecular chaperones: mediators of protein conformation and turnover in the cell. Cell. 1994 Aug 12;78(3):365–372. doi: 10.1016/0092-8674(94)90416-2. [DOI] [PubMed] [Google Scholar]
  11. Cyr D. M., Langer T., Douglas M. G. DnaJ-like proteins: molecular chaperones and specific regulators of Hsp70. Trends Biochem Sci. 1994 Apr;19(4):176–181. doi: 10.1016/0968-0004(94)90281-x. [DOI] [PubMed] [Google Scholar]
  12. Fields C., Adams M. D., White O., Venter J. C. How many genes in the human genome? Nat Genet. 1994 Jul;7(3):345–346. doi: 10.1038/ng0794-345. [DOI] [PubMed] [Google Scholar]
  13. Fodor S. P., Read J. L., Pirrung M. C., Stryer L., Lu A. T., Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science. 1991 Feb 15;251(4995):767–773. doi: 10.1126/science.1990438. [DOI] [PubMed] [Google Scholar]
  14. Gress T. M., Hoheisel J. D., Lennon G. G., Zehetner G., Lehrach H. Hybridization fingerprinting of high-density cDNA-library arrays with cDNA pools derived from whole tissues. Mamm Genome. 1992;3(11):609–619. doi: 10.1007/BF00352477. [DOI] [PubMed] [Google Scholar]
  15. Guo Z., Guilfoyle R. A., Thiel A. J., Wang R., Smith L. M. Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res. 1994 Dec 11;22(24):5456–5465. doi: 10.1093/nar/22.24.5456. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Jakob U., Buchner J. Assisting spontaneity: the role of Hsp90 and small Hsps as molecular chaperones. Trends Biochem Sci. 1994 May;19(5):205–211. doi: 10.1016/0968-0004(94)90023-x. [DOI] [PubMed] [Google Scholar]
  17. Jindal S. Heat shock proteins: applications in health and disease. Trends Biotechnol. 1996 Jan;14(1):17–20. doi: 10.1016/0167-7799(96)80909-7. [DOI] [PubMed] [Google Scholar]
  18. Liou H. C., Baltimore D. Regulation of the NF-kappa B/rel transcription factor and I kappa B inhibitor system. Curr Opin Cell Biol. 1993 Jun;5(3):477–487. doi: 10.1016/0955-0674(93)90014-h. [DOI] [PubMed] [Google Scholar]
  19. Matson R. S., Rampal J., Pentoney S. L., Jr, Anderson P. D., Coassin P. Biopolymer synthesis on polypropylene supports: oligonucleotide arrays. Anal Biochem. 1995 Jan 1;224(1):110–116. doi: 10.1006/abio.1995.1014. [DOI] [PubMed] [Google Scholar]
  20. Newton A. C. Protein kinase C: structure, function, and regulation. J Biol Chem. 1995 Dec 1;270(48):28495–28498. doi: 10.1074/jbc.270.48.28495. [DOI] [PubMed] [Google Scholar]
  21. Nishizuka Y. Protein kinase C and lipid signaling for sustained cellular responses. FASEB J. 1995 Apr;9(7):484–496. [PubMed] [Google Scholar]
  22. Rohan P. J., Davis P., Moskaluk C. A., Kearns M., Krutzsch H., Siebenlist U., Kelly K. PAC-1: a mitogen-induced nuclear protein tyrosine phosphatase. Science. 1993 Mar 19;259(5102):1763–1766. doi: 10.1126/science.7681221. [DOI] [PubMed] [Google Scholar]
  23. Schena M., Davis R. W. HD-Zip proteins: members of an Arabidopsis homeodomain protein superfamily. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3894–3898. doi: 10.1073/pnas.89.9.3894. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Schena M., Davis R. W. Structure of homeobox-leucine zipper genes suggests a model for the evolution of gene families. Proc Natl Acad Sci U S A. 1994 Aug 30;91(18):8393–8397. doi: 10.1073/pnas.91.18.8393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Schena M. Genome analysis with gene expression microarrays. Bioessays. 1996 May;18(5):427–431. doi: 10.1002/bies.950180513. [DOI] [PubMed] [Google Scholar]
  26. Schena M., Shalon D., Davis R. W., Brown P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995 Oct 20;270(5235):467–470. doi: 10.1126/science.270.5235.467. [DOI] [PubMed] [Google Scholar]
  27. 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 Jul;6(7):639–645. doi: 10.1101/gr.6.7.639. [DOI] [PubMed] [Google Scholar]
  28. Southern E. M., Maskos U., Elder J. K. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics. 1992 Aug;13(4):1008–1017. doi: 10.1016/0888-7543(92)90014-j. [DOI] [PubMed] [Google Scholar]
  29. Thanos D., Maniatis T. NF-kappa B: a lesson in family values. Cell. 1995 Feb 24;80(4):529–532. doi: 10.1016/0092-8674(95)90506-5. [DOI] [PubMed] [Google Scholar]
  30. Velculescu V. E., Zhang L., Vogelstein B., Kinzler K. W. Serial analysis of gene expression. Science. 1995 Oct 20;270(5235):484–487. doi: 10.1126/science.270.5235.484. [DOI] [PubMed] [Google Scholar]
  31. Watson J. D. Looking forward. Gene. 1993 Dec 15;135(1-2):309–315. doi: 10.1016/0378-1119(93)90083-f. [DOI] [PubMed] [Google Scholar]
  32. Wilkinson K. D. Roles of ubiquitinylation in proteolysis and cellular regulation. Annu Rev Nutr. 1995;15:161–189. doi: 10.1146/annurev.nu.15.070195.001113. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES

  NODES
Project 2
twitter 2