Skip to main content
SpringerLink
Log in

Microarray Analysis of Ethanol-Induced Changes in Gene Expression

  • Protocol
Alcohol

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 447))

Summary

DNA microarray studies offer a robust method for nonbiased analysis of whole genome messenger ribonucleic acid expression patterns. A growing number of studies have applied this experimental approach to studies on ethanol either in cell culture of animal models of ethanol exposure or self-administration. Expression profiling has identified novel gene networks responding to ethanol or differing across animal strains with differing responses to ethanol. Recent studies have shown benefit for meta-analysis of microarray data across different laboratories. Gene network analysis offers unique opportunities for understanding the molecular mechanisms of ethanol responses, toxicity and addiction. Eventually, such work may generate novel targets for future pharmacotherapy. To fully capitalize on the prom ise alluded to above, particularly in regard to meta-analysis of microarray data, it is critical that high quality standards are followed in the generation and analysis of microarray studies. This chapter will discuss experience of our laboratory in performing and analyzing microarray studies on ethanol, focusing discussion mainly on short oligonucleotide microarrays (Affymetrix). However, the general principals of technique and analysis that are discussed have broad applicability to other types of microarray platforms and experimental designs.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. 1. Nestler, E. J., and Aghajanian, G. K. (1997) Molecular and cellular basis of addiction. Science 278, 58–63.

    Article  PubMed  CAS  Google Scholar 

  2. 2. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P. O., and Davis, R. W. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA 93, 10614–10619.

    Article  PubMed  CAS  Google Scholar 

  3. 3. Lockhart, D. J., Dong, H., Byrne, M. C., et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14, 1675–1680.

    Article  PubMed  CAS  Google Scholar 

  4. 4.Quackenbush, J. (2001) Computational analysis of microarray data. Nat. Rev. Genet. 2, 418–427.

    Article  PubMed  CAS  Google Scholar 

  5. 5. 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.

    Article  PubMed  CAS  Google Scholar 

  6. 6.Hughes, T. R., Marton, M. J., Jones, A. R., et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102, 109–126.

    Article  PubMed  CAS  Google Scholar 

  7. 7.Thibault, C., Lai, C., Wilke, N., et al. (2000) Expression profiling of neural cells reveals specific patterns of ethanol-responsive gene expression. Mol. Pharmacol. 58, 1593–1600.

    PubMed  CAS  Google Scholar 

  8. 8.Hassan, S., Duong, B., Kim, K. S., and Miles, M. F. (2003) Pharmacogenomic analysis of mechanisms mediating ethanol regulation of dopamine beta-hydroxylase. J. Biol. Chem. 278, 38860–29969.

    Article  PubMed  CAS  Google Scholar 

  9. 9.Rimondini, R., Arlinde, C., Sommer, W., and Heilig, M. (2002) Long-lasting increase in voluntary ethanol consumption and transcriptional regulation in the rat brain after intermittent exposure to alcohol. FASEB J. 16, 27–35.

    Article  PubMed  CAS  Google Scholar 

  10. 10.Saito, M., Smiley, J., Toth, R., and Vadas, C. (2002) Microarray analysis of gene expression in rat hippocampus after chronic ethanol treatment. Neurochem. Res. 27, 1221–1229.

    Article  PubMed  CAS  Google Scholar 

  11. 11.Tadic, S. D., Elm, M. S., Li, H. S., et al. (2002) Sex differences in hepatic gene expression in a rat model of ethanol-induced liver injury. J. Appl. Physiol. 93, 1057–1068.

    PubMed  CAS  Google Scholar 

  12. 12.Daniels, G. M., and Buck, K. J. (2002) Expression profiling identifies strain-specific changes associated with ethanol withdrawal in mice. Genes Brain Behav, 1, 35–45.

    Article  CAS  Google Scholar 

  13. 13.Tabakoff, B., Bhave, S. V., and Hoffman, P. L. (2003) Selective breeding, quantitative trait locus analysis, and gene arrays identify candidate genes for complex drug-related behaviors. J. Neurosci. 23, 4491–4498.

    PubMed  CAS  Google Scholar 

  14. 14.Treadwell, J. A., and Singh, S. M. (2004) Microarray analysis of mouse brain gene expression following acute ethanol treatment. Neurochem. Res. 29, 357–369.

    Article  PubMed  CAS  Google Scholar 

  15. 15.Kerns, R. T., Ravindranathan, A., Hassan, S., et al. (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. J. Neurosci. 25, 2255–2266.

    Article  PubMed  CAS  Google Scholar 

  16. 16.Lewohl, J. M., Wang, L., Miles, M. F., Zhang, L., Dodd, P. R., and Harris, R. A. (2000) Gene expression in human alcoholism: microarray analysis of frontal cortex. Alcohol. Clin. Exp. Res. 24, 1873–1882.

    Article  PubMed  CAS  Google Scholar 

  17. 17.Mayfield, R. D., Lewohl, J. M., Dodd, P. R., Herlihy, A., Liu, J., and Harris, R. A. (2002) Patterns of gene expression are altered in the frontal and motor cortices of human alcoholics. J. Neurochem. 81, 802–813.

    Article  PubMed  CAS  Google Scholar 

  18. 18.Mulligan, M. K., Ponomarev, I., Hitzemann, R. J., et al. (2006) Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. Proc. Natl. Acad. Sci. USA 103, 6368–6373.

    Article  PubMed  CAS  Google Scholar 

  19. 19.Chesler, E. J., Wang, J., Lu, L., Qu, Y., Manly, K. F., and Williams, R. W. (2003) Genetic correlates of gene expression in recombinant inbred strains: a relational model system to explore neurobehavioral phenotypes. Neuroinformatics 1, 343–357.

    Article  PubMed  Google Scholar 

  20. 20.Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470.

    Article  PubMed  CAS  Google Scholar 

  21. 21.Barnes, M., Freudenberg, J., Thompson, S., Aronow, B., and Pavlidis, P. (2005) Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic. Acids Res. 33, 5914–5923.

    Article  PubMed  CAS  Google Scholar 

  22. 22.Van Gelder, R. N., von Zastrow, M. E., Yool, A., Dement, W. C., Barchas, J. D., and Eberwine, J. H. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. USA 87, 1663–1667.

    Article  PubMed  CAS  Google Scholar 

  23. 23.Kacharmina, J. E., Crino, P. B., and Eberwine, J. (1999) Preparation of cDNA from single cells and subcellular regions. Methods Enzymol. 303, 3–18.

    Article  PubMed  CAS  Google Scholar 

  24. 24.Yang, Y. H., and Speed, T. (2002) Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3, 579–588.

    PubMed  CAS  Google Scholar 

  25. 25.Lee, M. L., Kuo, F. C., Whitmore, G. A., and Sklar, J. (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA 97, 9834–9839.

    Article  PubMed  CAS  Google Scholar 

  26. 26.Dudoit, S., Yang, Y. H., Callow, M. J., and Speed, T. J. (2000) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Technical Report. Stanford, CA: Stanford University School of Medicine; Report No. 578.

    Google Scholar 

  27. 27.Luo, L., Salunga, R. C., Guo, H., et al. (1999) Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat. Med. 5, 117–122.

    Article  PubMed  CAS  Google Scholar 

  28. 28.Sandberg, R., Yasuda, R., Pankratz, D. G., et al. (2000) Regional and strain-specific gene expression mapping in the adult mouse brain. Proc. Natl. Acad. Sci. USA 97, 11038–11043.

    Article  PubMed  CAS  Google Scholar 

  29. 29.Geschwind, D. H. (2000) Mice, microarrays, and the genetic diversity of the brain. Proc. Natl. Acad. Sci. USA 97, 10676–10678.

    Article  PubMed  CAS  Google Scholar 

  30. 30.Wahlsten, D., Metten, P., Phillips, T. J., et al. (2003) Different data from different labs: lessons from studies of gene-environment interaction. J. Neurobiol. 54, 283–311.

    Article  PubMed  Google Scholar 

  31. 31.Irizarry, R. A., Bolstad, B. M., Collin, F., Cope, L. M., Hobbs, B., and Speed, T. P. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15.

    Article  PubMed  Google Scholar 

  32. 32.Li, C., and Wong, W. H. (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 98, 31–36.

    Article  PubMed  CAS  Google Scholar 

  33. 33.Zhang, L., Miles, M. F., and Aldape, K. D. (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat. Biotechnol. 21, 818–821.

    Article  PubMed  CAS  Google Scholar 

  34. 34.Zhang, L., Wang, L., Ravindranathan, A., and Miles, M. F. (2002) A new algorithm for analysis of oligonucleotide arrays: Application to expression profiling in mouse brain regions. J. Mol. Biol. 317, 225–235.

    Article  PubMed  CAS  Google Scholar 

  35. 35.Kerns, R. T., Zhang, L., and Miles, M. F. (2003) Application of the S-score algorithm for analysis of oligonucleotide microarrays. Methods 31, 274–281.

    Article  PubMed  CAS  Google Scholar 

  36. 36.Kennedy, R. E., Kerns, R. T., Kong, X., Archer, K. J., and Miles, M. F. (2006) SScore: an R package for detecting differential gene expression without gene expression summaries. Bioinformatics 22, 1272–1274.

    Article  PubMed  CAS  Google Scholar 

  37. 37.Kennedy, R. E., Archer, K. J., and Miles, M. F. (2006) Empirical validation of the S-score algorithm in the analysis of gene expression data. BMC Bioinformatics 7:154.

    Article  PubMed  Google Scholar 

  38. 38.Kim, S. Y., Lee, J. W., and Sohn, I. S. (2006) Comparison of various statistical methods for identifying differential gene expression in replicated microarray data. Stat. Methods Med. Res. 15, 3–20.

    Article  PubMed  Google Scholar 

  39. 39.Reimers, M. (2005) Statistical analysis of microarray data. Addict. Biol. 10, 23–35.

    Article  PubMed  CAS  Google Scholar 

  40. 40.Tusher, V. G., Tibshirani, R., Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98, 5116–5121.

    Article  PubMed  CAS  Google Scholar 

  41. 41.Saeed, A. I., Sharov, V., White, J., et al. (2003) TM4: a free, open-source system for microarray data management and analysis. BioTechniques 34, 374–378.

    PubMed  CAS  Google Scholar 

  42. 42.Consortium TGO. (2001) Creating the gene ontology resource: design and implementation. Genome Res. 11, 1425–1433.

    Article  Google Scholar 

  43. 43.Doniger, S. W., Salomonis, N., Dahlquist, K. D., Vranizan, K., Lawlor, S. C., and Conklin, B. R. (2003) MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome. Biol. 4:R7.

    Article  PubMed  Google Scholar 

  44. 44.Hosack, D. A., Dennis, G., Jr., Sherman, B. T., Lane, H. C., and Lempicki, R. A. (2003) Identifying biological themes within lists of genes with EASE. Genome Biol. 4:R70.

    Article  PubMed  Google Scholar 

  45. 45.Pavlidis, P., Qin, J., Arango, V., Mann, J. J., Sibille, E. (2004) Using the gene ontology for microarray data mining: A comparison of methods and application to age effects in human prefrontal cortex. Neurochem. Res . 29, 1213–1222.

    Article  PubMed  CAS  Google Scholar 

  46. 46.Zhang, B., Kirov, S., and Snoddy, J. (2005) WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 33(Web Server issue), W741–W748.

    Article  PubMed  CAS  Google Scholar 

  47. 47.Chen, H., and Sharp, B. M. (2004) Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics 5, 147.

    Article  PubMed  Google Scholar 

  48. 48.Chesler, E. J., Lu, L., Wang, J., Williams, R. W., and Manly, K. F. (2004) WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nat. Neurosci. 7, 485–486.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by NIAAA Grants RO1 AA014717 to MFM and F32 AA014726 to RTK.

Author information

Authors and Affiliations

  1. Departments of Pharmacology/Toxicology and Neurology, and the Center for Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA

    Robnet T. Kerns PhD & Michael F. Miles MD,PhD

Authors
  1. Robnet T. Kerns PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael F. Miles MD,PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Departments of Gastroenterology and Pathobiology Cleveland Clinic and Department of Nutrition, Case Western Reserve University, Cleveland, USA

    Laura E. Nagy

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Kerns, R.T., Miles, M.F. (2008). Microarray Analysis of Ethanol-Induced Changes in Gene Expression. In: Nagy, L.E. (eds) Alcohol. Methods in Molecular Biology™, vol 447. Humana Press. https://doi.org/10.1007/978-1-59745-242-7_26

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-242-7_26

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-906-2

  • Online ISBN: 978-1-59745-242-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation