Gene Expression Analysis

  • David S. Skibbe
  • Virginia Walbot

A brief history of methods used to elucidate protein function, protein presence, and RNA transcript presence is provided. Gene expression profiling through microarray hybridization, high throughput sequencing, or quantitative reverse transcriptase-polymerase chain reaction methods are reviewed and compared. Proteomics analysis using two dimensional gel electrophoresis followed by protein identification by mass spectrometry is then discussed. Relative costs and prospects for future improvements are also presented.


Gene Expression Analysis Shoot Apical Meristem Transcriptome Profile Laser Microdissection Maize Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Chalkley, R.J., P.R. Baker, K.C. Hansen, K.F. Medzihradszky, N.P. Allen, M. Rexach and A.L. Burlingame (2005) Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting quadrupole collision cell, time-of-flight mass spectrometer. I. How much of the data is theoretically interpretable by search engines? Mol. Cell. Proteomics 4: 1189–1193.PubMedCrossRefGoogle Scholar
  2. Chalkley, R.J., P.R. Baker, L. Huang, K.C. Hansen, N.P. Allen, M. Rexach and A.L. Burlingame (2005) Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting quadrupole collision cell, time-of-flight mass spectrometer. II. New developments in protein prospector allow for reliable and comprehensive automatic analysis of large datasets. Mol. Cell. Proteomics 4: 1194–1204.PubMedCrossRefGoogle Scholar
  3. Czechowski, T., R.P. Bari, M. Stitt, W.-R. Scheible and M.K. Udvardi (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J. 38: 366–379.PubMedCrossRefGoogle Scholar
  4. Day, R.C., U. Grossniklaus and R.C. Macknight, (2005) Be more specific! Laser-assisted microdissection of plant cells. Trends Plant Sci. 10: 397–406.PubMedCrossRefGoogle Scholar
  5. Dodd, L.E., E.L. Korn, L.M. McShane, G.V.R. Chandramouli and E.Y. Chuang (2004) Correcting log ratios for signal saturation in cDNA microarrays. Bioinformatics 20: 2685–2693.PubMedCrossRefGoogle Scholar
  6. Dudley, A., J. Aach, M. Steffen and G. Church (2002) Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99: 7754–7759.Google Scholar
  7. Jiang, K., S. Zhang, S. Lee, G. Tsai, K. Kim, H. Huang, C. Chilcott, T. Zhu and L.J. Feldman (2006) Transcription profile analyses identify genes and pathways central to root cap functions in maize. Plant Mol. Biol. 60: 343–363.PubMedCrossRefGoogle Scholar
  8. Kehr, J. (2003) Single cell technology. Curr. Opin. Plant Biol. 6: 617–621.PubMedCrossRefGoogle Scholar
  9. Kerk, N.M., T. Ceserani, S.L. Tausta, I.M. Sussex and T.M. Nelson (2003) Laser capture microdis-section of cells from plant tissues. Plant Physiol. 132: 27–35.PubMedCrossRefGoogle Scholar
  10. Liu, Y., T. Lamkemeyer, A. Jakob, G. Mi, F. Zhang, A. Nordheim and F. Hochholdinger (2006) Comparative proteome analyses of maize (Zea mays L.) primary roots prior to lateral root initiation reveal differential protein expression in the lateral root initiation mutant rum1.Proteomics 6: 4300–4308.PubMedCrossRefGoogle Scholar
  11. Nakazono, M., F. Qiu, L.A. Borsuk and P.S. Schnable (2003) Laser—capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell 3: 583–596.CrossRefGoogle Scholar
  12. Nelson, T., S.L. Tausta, N. Gandotra and T. Liu (2006) Laser microdissection of plant tissue: what you see is what you get. Annu. Rev. Plant Biol. 57: 181–201.PubMedCrossRefGoogle Scholar
  13. Ohtsu, K., M.B. Smith, S.J. Emrich, L.A. Borsuk, R. Zhou, T. Chen, X. Zhang, M. Timmermans, J. Beck, B. Buckner, D. Janick-Buckner, D. Nettleton, M.J. Scanlon and P.S. Schnable (2007) Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). Plant J., in press.Google Scholar
  14. Ohtsu, K., H. Takahashi, P.S. Schnable and M. Nakazono (2007) Cell type-specific gene expression profiling in plants by using a combination of laser microdissection and high-throughput technologies. Plant Cell Physiol. 48: 3–7.PubMedCrossRefGoogle Scholar
  15. Schena, M., D. Shalon, R.W. Davis, and P.O. Brown (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470.PubMedCrossRefGoogle Scholar
  16. Schnable P.S., M. Nakazono, and F. Hochholdinger (2004) Global expression profiling applied to plant development. Curr. Opin. Plant Biol. 7: 50–56.PubMedCrossRefGoogle Scholar
  17. Skibbe, D.S., X. Wang, X. Zhao, L.A. Borsuk, D. Nettleton and P.S. Schnable (2006) Scanning microarrays at multiple intensities enhances discovery of differentially expressed gene. Bioinformatics 22: 1863–1870.PubMedCrossRefGoogle Scholar
  18. Woll, K., L.A. Borsuk, H. Stransky, D. Nettleton, P.S. Schnable and F. Hochholdinger (2005) Isolation, characterization and pericycle specific transcriptome analyses of the novel maize (Zea mays L.) lateral and seminal root initiation mutant rum1. Plant Physiol. 139: 1255–1267.PubMedCrossRefGoogle Scholar
  19. Zhang, X., S. Medi, L.A. Borsuk, D. Nettleton, B. Buckner, D. Janick-Buckner, J. Beck, M. Timmermans, P.S. Schnable and M.J. Scanlon (2007) Laser microdissection of narrow sheath mutant maize uncovers novel gene expression in the shoot apical meristem. PLoS Genetics 3: 1040–1052.CrossRefGoogle Scholar

Copyright information

© Springer Science + Business Media, LLC 2009

Authors and Affiliations

  1. 1.Department of BiologyStanford UniversityCalifornia

Personalised recommendations