Skip to main content
SpringerLink
Log in

Microarray-Based Identification of Transcription Factor Target Genes

  • Protocol
  • First Online:
Plant Transcription Factors

Part of the book series: Methods in Molecular Biology ((MIMB,volume 754))

Abstract

Microarray analysis is widely used to identify transcriptional changes associated with genetic perturbation or signaling events. Here we describe its application in the identification of plant transcription factor target genes with emphasis on the design of suitable DNA constructs for controlling TF activity, the experimental setup, the statistical analysis of the microarray data, and the validation of target genes.

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 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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. Gregory, B. D., and Belostotsky, D. A. (2009) Whole-genome microarrays: applications and technical issues. Methods Mol. Biol. 553, 39–56.

    Article  PubMed  CAS  Google Scholar 

  2. Wang, Z., Gerstein, M., and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63.

    Article  PubMed  CAS  Google Scholar 

  3. Collas, P. (2010) The current state of chromatin immunoprecipitation. Mol. Biotechnol. 45, 87–100.

    Article  PubMed  CAS  Google Scholar 

  4. Kirmizis, A., and Farnham, P. J. (2004) Genomic approaches that aid in the identification of transcription factor target genes. Exp. Biol. Med. (Maywood). 229, 705–721.

    CAS  Google Scholar 

  5. Aranda, A., and Pascual, A. (2001) Nuclear hormone receptors and gene expression. Physiol. Rev. 81, 1269–1304.

    PubMed  CAS  Google Scholar 

  6. Gomez-Mena, C., de Folter, S., Costa, M. M. R., Angenent, G. C., and Sablowski, R. (2005) Transcriptional program controlled by the floral homeotic gene AGAMOUS during early organogenesis. Development 132, 429–438.

    Article  PubMed  CAS  Google Scholar 

  7. Wagner, D., Wellmer, F., Dilks, K., William, D., Smith, M. R., Kumar, P. P., Riechmann, J. L., Greenland, A. J., and Meyerowitz, E. M. (2004) Floral induction in tissue culture: a system for the analysis of LEAFY-dependent gene regulation. Plant J. 39, 273–282.

    Article  PubMed  CAS  Google Scholar 

  8. Passarinho, P., Ketelaar, T., Xing, M., van Arkel, J., Maliepaard, C., Hendriks, M. W., Joosen, R., Lammers, M., Herdies, L., den Boer, B., van der Geest, L., and Boutilier, K. (2008) BABY BOOM target genes provide diverse entry points into cell proliferation and cell growth pathways. Plant Mol. Biol. 68, 225–237.

    Article  PubMed  CAS  Google Scholar 

  9. Rohila, J. S., Chen, M., Cerny, R., and Fromm, M. E. (2004) Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants. Plant J. 38, 172–181.

    Article  PubMed  CAS  Google Scholar 

  10. Craft, J., Samalova, M., Baroux, C., Townley, H., Martinez, A., Jepson, I., Tsiantis, M., and Moore, I. (2005) New pOp/LhG4 vectors for stringent glucocorticoid-dependent transgene expression in Arabidopsis. Plant J. 41, 899–918.

    Article  PubMed  CAS  Google Scholar 

  11. Hanson, J., Hanssen, M., Wiese, A., Hendriks, M. M., and Smeekens, S. (2008) The sucrose regulated transcription factor bZIP11 affects amino acid metabolism by regulating the expression of ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2. Plant J. 53, 935–949.

    Article  PubMed  CAS  Google Scholar 

  12. Aoyama, T., and Chua, N. H. (1997) A glucocorticoid-mediated transcriptional induction system in transgenic plants. Plant J. 11, 605–612.

    Article  PubMed  CAS  Google Scholar 

  13. Levesque, M. P., Vernoux, T., Busch, W., Cui, H., Wang, J. Y., Blilou, I., Hassan, H., Nakajima, K., Matsumoto, N., Lohmann, J. U., Scheres, B., and Benfey, P. N. (2006) Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol. 4, e143.

    Article  PubMed  Google Scholar 

  14. Hay, A., Jackson, D., Ori, N., and Hake, S. (2003) Analysis of the competence to respond to KNOTTED1 activity in Arabidopsis leaves using a steroid induction system. Plant Physiol. 131, 1671–1680.

    Article  PubMed  CAS  Google Scholar 

  15. Sundstrom, J. F., Nakayama, N., Glimelius, K., and Irish, V. F. (2006) Direct regulation of the floral homeotic APETALA1 gene by APETALA3 and PISTILLATA in Arabidopsis. Plant J. 46, 593–600.

    Article  PubMed  CAS  Google Scholar 

  16. Ikeda, Y., Banno, H., Niu, Q. W., Howell, S. H., and Chua, N. H. (2006) The ENHANCER OF SHOOT REGENERATION 2 gene in Arabidopsis regulates CUP-SHAPED COTYLEDON 1 at the transcriptional level and controls cotyledon development. Plant Cell Physiol. 47, 1443–1456.

    Article  PubMed  CAS  Google Scholar 

  17. Che, P., Lall, S., and Howell, S. H. (2008) Acquiring competence for shoot development in Arabidopsis: ARR2 directly targets A-type ARR genes that are differentially activated by CIM preincubation. Plant Signal. Behav. 3, 99–101.

    Article  PubMed  Google Scholar 

  18. Zuo, J., Niu, Q. W., and Chua, N. H. (2000) Technical advance: an estrogen receptor-based transactivator XVE mediates highly inducible gene expression in transgenic plants. Plant J. 24, 265–273.

    Article  PubMed  CAS  Google Scholar 

  19. Tornero, P., Chao, R. A., Luthin, W. N., Goff, S. A., and Dangl, J. L. (2002) Large-scale structure–function analysis of the Arabidopsis RPM1 disease resistance protein. Plant Cell 14, 435–450.

    Article  PubMed  CAS  Google Scholar 

  20. Zuo, J., and Chua, N. H. (2000) Chemical-inducible systems for regulated expression of plant genes. Curr. Opin. Biotechnol. 11, 146–151.

    Article  PubMed  CAS  Google Scholar 

  21. Gatz, C., and Lenk, I. (1998) Promoters that respond to chemical inducers. Trends Plant Sci. 3, 352–358.

    Article  Google Scholar 

  22. Ko, J. H., Kim, W. C., and Han, K. H. (2009) Ectopic expression of MYB46 identifies transcriptional regulatory genes involved in secondary wall biosynthesis in Arabidopsis. Plant J. 60, 649–665.

    Article  PubMed  CAS  Google Scholar 

  23. Zentella, R., Zhang, Z. L., Park, M., Thomas, S. G., Endo, A., Murase, K., Fleet, C. M., Jikumaru, Y., Nambara, E., Kamiya, Y., and Sun, T. P. (2007) Global analysis of della direct targets in early gibberellin signaling in Arabidopsis. Plant Cell 19, 3037–3057.

    Article  PubMed  CAS  Google Scholar 

  24. Kang, H. G., Fang, Y., and Singh, K. B. (1999) A glucocorticoid-inducible transcription system causes severe growth defects in Arabidopsis and induces defense-related genes. Plant J. 20, 127–133.

    Article  PubMed  CAS  Google Scholar 

  25. Ouwerkerk, P. B., de Kam, R. J., Hoge, J. H., and Meijer, A. H. (2001) Glucocorticoid-inducible gene expression in rice. Planta 213, 370–378.

    Article  PubMed  CAS  Google Scholar 

  26. Andersen, S. U., Cvitanich, C., Hougaard, B. K., Roussis, A., Gronlund, M., Jensen, D. B., Frokjaer, L. A., and Jensen, E. O. (2003) The glucocorticoid-inducible GVG system causes severe growth defects in both root and shoot of the model legume Lotus japonicus. Mol. Plant Microbe Interact. 16, 1069–1076.

    Article  PubMed  CAS  Google Scholar 

  27. Weijers, D., Van Hamburg, J. P., Van Rijn, E., Hooykaas, P. J., and Offringa, R. (2003) Diphtheria toxin-mediated cell ablation reveals interregional communication during Arabidopsis seed development. Plant Physiol. 133, 1882–1892.

    Article  PubMed  CAS  Google Scholar 

  28. Galweiler, L., Conlan, R. S., Mader, P., Palme, K., and Moore, I. (2000) Technical advance: the DNA-binding activity of gal4 is inhibited by methylation of the gal4 binding site in plant chromatin. Plant J. 23, 143–157.

    Article  PubMed  CAS  Google Scholar 

  29. Engineer, C. B., Fitzsimmons, K. C., Schmuke, J. J., Dotson, S. B., and Kranz, R. G. (2005) Development and evaluation of a Gal4-mediated LUC/GFP/GUS enhancer trap system in Arabidopsis. BMC Plant Biol. 5, 9.

    Article  PubMed  Google Scholar 

  30. Liu, C., Chen, H., Er, H. L., Soo, H. M., Kumar, P. P., Han, J. H., Liou, Y. C., and Yu, H. (2008) Direct interaction of AGL24 and SOC1 integrates flowering signals in Arabidopsis. Development 135, 1481–1491.

    Article  PubMed  CAS  Google Scholar 

  31. Matsuo, N., Mase, H., Makino, M., Takahashi, H., and Banno, H. (2009) Identification of ENHANCER OF SHOOT REGENERATION 1-upregulated genes during in vitro shoot regeneration. Plant Biotechnol. 26, 385–393.

    Article  CAS  Google Scholar 

  32. Pre, M., Atallah, M., Champion, A., De Vos, M., Pieterse, C. M. J., and Memelink, J. (2008) The AP2/ERF domain transcription factor ORA59 integrates jasmonic acid and ethylene signals in plant defense. Plant Physiol. 147, 1347–1357.

    Article  PubMed  CAS  Google Scholar 

  33. Balazadeh, S., Siddiqui, H., Allu, A. D., Matallana-Ramirez, L. P., Caldana, C., Mehrnia, M., Zanor, M. I., Kohler, B., and Mueller-Roeber, B. (2010) A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. Plant J. 62, 250–264.

    Article  PubMed  CAS  Google Scholar 

  34. Turner, R., and Foster, G. D. (1995) The potential exploitation of plant viral translational enhancers in biotechnology for increased gene-expression. Mol. Biotechnol. 3, 225–236.

    Article  PubMed  CAS  Google Scholar 

  35. Zhong, R., Richardson, E. A., and Ye, Z. H. (2007) The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis. Plant Cell 19, 2776–2792.

    Article  PubMed  CAS  Google Scholar 

  36. McKeehan, W., and Hardesty, B. (1969) The mechanism of cycloheximide inhibition of protein synthesis in rabbit reticulocytes. Biochem. Biophys. Res. Commun. 36, 625–630.

    Article  PubMed  CAS  Google Scholar 

  37. Lee, D. J., Park, J. W., Lee, H. W., and Kim, J. (2009) Genome-wide analysis of the auxin-responsive transcriptome downstream of iaa1 and its expression analysis reveal the diversity and complexity of auxin-regulated gene expression. J. Exp. Bot. 60, 3935–3957.

    Article  PubMed  CAS  Google Scholar 

  38. Ravni, A., Eiden, L. E., Vaudry, H., Gonzalez, B. J., and Vaudry, D. (2006) Cycloheximide treatment to identify components of the transitional transcriptome in PACAP-induced PC12 cell differentiation. J. Neurochem. 98, 1229–1241.

    Article  PubMed  CAS  Google Scholar 

  39. Abel, S., Nguyen, M. D., and Theologis, A. (1995) The PS-IAA4/5-like family of early auxin-inducible mRNAs in Arabidopsis thaliana. J. Mol. Biol. 251, 533–549.

    Article  PubMed  CAS  Google Scholar 

  40. Theologis, A., Huynh, T. V., and Davis, R. W. (1985) Rapid induction of specific mRNAs by auxin in pea epicotyl tissue. J. Mol. Biol. 183, 53–68.

    Article  PubMed  CAS  Google Scholar 

  41. Herrick, D., Parker, R., and Jacobson, A. (1990) Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae. Mol. Cell Biol. 10, 2269–2284.

    PubMed  CAS  Google Scholar 

  42. Kiddle, S. J., Windram, O. P., McHattie, S., Mead, A., Beynon, J., Buchanan-Wollaston, V., Denby, K. J., and Mukherjee, S. (2010) Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana. Bioinformatics 26, 355–362.

    Article  PubMed  CAS  Google Scholar 

  43. Herzenberg, L. A., Sweet, R. G., and Herzenberg, L. A. (1976) Fluorescence-activated cell sorting. Sci. Am. 234, 108–117.

    Article  PubMed  CAS  Google Scholar 

  44. Bargmann, B. O., and Birnbaum, K. D. (2009) Fluorescence activated cell sorting of plant protoplasts. JoVE. 36. http://www.jove.com/index/Details.stp?ID=1673. doi: 10.3791/1673.

  45. Birnbaum, K., Jung, J. W., Wang, J. Y., Lambert, G. M., Hirst, J. A., Galbraith, D. W., and Benfey, P. N. (2005) Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nat. Methods 2, 615–619.

    Article  PubMed  CAS  Google Scholar 

  46. Birnbaum, K., Shasha, D. E., Wang, J. Y., Jung, J. W., Lambert, G. M., Galbraith, D. W., and Benfey, P. N. (2003) A gene expression map of the Arabidopsis root. Science 302, 1956–1960.

    Article  PubMed  CAS  Google Scholar 

  47. Yadav, R. K., Girke, T., Pasala, S., Xie, M., and Reddy, G. V. (2009) Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proc. Natl. Acad. Sci. USA 106, 4941–4946.

    Article  PubMed  CAS  Google Scholar 

  48. Sheen, J. (2001) Signal transduction in maize and Arabidopsis mesophyll protoplasts. Plant Physiol. 127, 1466–1475.

    Article  PubMed  CAS  Google Scholar 

  49. Rajeevan, M. S., Ranamukhaarachchi, D. G., Vernon, S. D., and Unger, E. R. (2001) Use of real-time quantitative PCR to validate the results of cDNA array and differential display PCR technologies. Methods 25, 443–451.

    Article  PubMed  CAS  Google Scholar 

  50. Chuaqui, R. F., Bonner, R. F., Best, C. J., Gillespie, J. W., Flaig, M. J., Hewitt, S. M., Phillips, J. L., Krizman, D. B., Tangrea, M. A., Ahram, M., Linehan, W. M., Knezevic, V., and Emmert-Buck, M. R. (2002) Post-analysis follow-up and validation of microarray experiments. Nat. Genet. 32 Suppl., 509–514.

    Article  PubMed  CAS  Google Scholar 

  51. Canales, R. D., Luo, Y., Willey, J. C., Austermiller, B., Barbacioru, C. C., Boysen, C., Hunkapiller, K., Jensen, R. V., Knight, C. R., Lee, K. Y., Ma, Y., Maqsodi, B., Papallo, A., Peters, E. H., Poulter, K., Ruppel, P. L., Samaha, R. R., Shi, L., Yang, W., Zhang, L., and Goodsaid, F. M. (2006) Evaluation of DNA microarray results with quantitative gene expression platforms. Nat. Biotechnol. 24, 1115–1122.

    Article  PubMed  CAS  Google Scholar 

  52. Bustin, S. A. (2002) Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J. Mol. Endocrinol. 29, 23–39.

    Article  PubMed  CAS  Google Scholar 

  53. Pfaffl, M. A. (2006) Relative quantification, in Real-time PCR (Dorak, M. T., Ed.), pp 63–82. Taylor and Francis, New York, NY.

    Google Scholar 

  54. Karlen, Y., McNair, A., Perseguers, S., Mazza, C., and Mermod, N. (2007) Statistical significance of quantitative PCR. BMC Bioinformatics 8, 131.

    Article  PubMed  Google Scholar 

  55. Bustin, S. A., and Nolan, T. (2004) Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J. Biomol. Tech. 15, 155–166.

    PubMed  Google Scholar 

  56. Bustin, S. A., Benes, V., Garson, J. A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M. W., Shipley, G. L., Vandesompele, J., and Wittwer, C. T. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55, 611–622.

    Article  PubMed  CAS  Google Scholar 

  57. Bustin, S. A., Benes, V., Nolan, T., and Pfaffl, M. W. (2005) Quantitative real-time RT-PCR—a perspective. J. Mol. Endocrinol. 34, 597–601.

    Article  PubMed  CAS  Google Scholar 

  58. Wong, M. L., and Medrano, J. F. (2005) Real-time PCR for mRNA quantitation. Biotechniques 39, 75–85.

    Article  PubMed  CAS  Google Scholar 

  59. Czechowski, T., Stitt, M., Altmann, T., Udvardi, M. K., and Scheible, W. R. (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol. 139, 5–17.

    Article  PubMed  CAS  Google Scholar 

  60. Gutierrez, L., Mauriat, M., Guenin, S., Pelloux, J., Lefebvre, J. F., Louvet, R., Rusterucci, C., Moritz, T., Guerineau, F., Bellini, C., and Van Wuytswinkel, O. (2008) The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol. J. 6, 609–618.

    Article  PubMed  CAS  Google Scholar 

  61. Freeman, W. M., Walker, S. J., and Vrana, K. E. (1999) Quantitative RT-PCR: pitfalls and potential. Biotechniques 26, 112–125.

    PubMed  CAS  Google Scholar 

  62. Beckman, K. B., Lee, K. Y., Golden, T., and Melov, S. (2004) Gene expression profiling in mitochondrial disease: assessment of microarray accuracy by high-throughput Q-PCR. Mitochondrion 4, 453–470.

    Article  PubMed  CAS  Google Scholar 

  63. Leibfried, A., To, J. P., Busch, W., Stehling, S., Kehle, A., Demar, M., Kieber, J. J., and Lohmann, J. U. (2005) WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulators. Nature 438, 1172–1175.

    Article  PubMed  CAS  Google Scholar 

  64. Schlereth, A., Moller, B., Liu, W., Kientz, M., Flipse, J., Rademacher, E. H., Schmid, M., Jurgens, G., and Weijers, D. (2010) MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor. Nature 464, 913–916.

    Google Scholar 

  65. Ye, Q., Zhu, W., Li, L., Zhang, S., Yin, Y., Ma, H., and Wang, X. (2010) Brassinosteroids control male fertility by regulating the expression of key genes involved in Arabidopsis anther and pollen development. Proc. Natl. Acad. Sci. USA 107, 6100–6105.

    Google Scholar 

  66. Kaufmann, K., Muino, J. M., Osteras, M., Farinelli, L., Krajewski, P., and Angenent, G. C. (2010) Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat. Protoc. 5, 457–472.

    Article  PubMed  CAS  Google Scholar 

  67. Fu, W. J., Stromberg, A. J., Viele, K., Carroll, R. J., and Wu, G. (2010) Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology. J. Nutr. Biochem. 21, 561–572.

    Article  PubMed  CAS  Google Scholar 

  68. Peng, X., Wood, C. L., Blalock, E. M., Chen, K. C., Landfield, P. W., and Stromberg, A. J. (2003) Statistical implications of pooling RNA samples for microarray experiments. BMC Bioinformatics 4, 26.

    Article  PubMed  Google Scholar 

  69. Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate – a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 57, 289–300.

    Google Scholar 

  70. Liu, H., Tarima, S., Borders, A. S., Getchell, T. V., Getchell, M. L., and Stromberg, A. J. (2005) Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments. BMC Bioinformatics 6, 106.

    Article  PubMed  Google Scholar 

  71. Skern, R., Frost, P., and Nilsen, F. (2005) Relative transcript quantification by quantitative PCR: roughly right or precisely wrong? BMC Mol. Biol. 6, 10.

    Article  PubMed  Google Scholar 

  72. Yuan, J. S., Reed, A., Chen, F., and Stewart, C. N., Jr. (2006) Statistical analysis of real-time PCR data. BMC Bioinformatics 7, 85.

    Article  PubMed  Google Scholar 

  73. Yuan, J. S., Wang, D., and Stewart, C. N., Jr. (2008) Statistical methods for efficiency adjusted real-time PCR quantification. Biotechnol. J. 3, 112–123.

    Article  PubMed  CAS  Google Scholar 

  74. Livak, K. J., and Schmittgen, T. D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25, 402–408.

    Article  PubMed  CAS  Google Scholar 

  75. Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., and Speleman, F. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3, RESEARCH0034.

    Article  PubMed  Google Scholar 

  76. Andersen, C. L., Jensen, J. L., and Orntoft, T. F. (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 64, 5245–5250.

    Article  PubMed  CAS  Google Scholar 

  77. Pfaffl, M. W. (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, e45.

    Article  PubMed  CAS  Google Scholar 

  78. Hellemans, J., Mortier, G., De Paepe, A., Speleman, F., and Vandesompele, J. (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 8, R19.

    Article  PubMed  Google Scholar 

  79. Burns, M. J., Nixon, G. J., Foy, C. A., and Harris, N. (2005) Standardisation of data from real-time quantitative PCR methods – evaluation of outliers and comparison of calibration curves. BMC Biotechnol. 5, 31.

    Article  PubMed  Google Scholar 

  80. Peirson, S. N., Butler, J. N., and Foster, R. G. (2003) Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis. Nucleic Acids Res. 31, e73.

    Article  PubMed  Google Scholar 

  81. Ramakers, C., Ruijter, J. M., Deprez, R. H., and Moorman, A. F. (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci. Lett. 339, 62–66.

    Article  PubMed  CAS  Google Scholar 

  82. Cikos, S., Bukovska, A., and Koppel, J. (2007) Relative quantification of mRNA: comparison of methods currently used for real-time PCR data analysis. BMC Mol. Biol. 8, 113.

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

M.G. was supported by a Netherlands Genomic Initiative Horizon grant. A.H. was supported by a Technology Top Institute Green Genetics grant. A.S. was supported by NIH P20 RR16481 and NSF EPS-0814194.

Author information

Authors and Affiliations

  1. Molecular Genetics Group, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands

    Maartje Gorte & Renze Heidstra

  2. Plant Research International, Wageningen, The Netherlands

    Anneke Horstman & Kim Boutilier

  3. Department of Biology, Auburn University, Montgomery, AL, USA

    Robert B. Page

  4. Department of Statistics, University of Kentucky, Lexington, KY, USA

    Arnold Stromberg

Authors
  1. Maartje Gorte
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anneke Horstman
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Robert B. Page
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Renze Heidstra
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Arnold Stromberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Kim Boutilier
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kim Boutilier .

Editor information

Editors and Affiliations

  1. College of Agriculture, Dept. Plant & Soil Sciences, University of Kentucky, University Drive 1401, Lexington, 40546-0236, Kentucky, USA

    Ling Yuan

  2. Dept. Plant & Soil Sciences, University of Kentucky, Veterans Dr. 1405, Lexington, 40546-0312, Kentucky, USA

    Sharyn E. Perry

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Gorte, M., Horstman, A., Page, R.B., Heidstra, R., Stromberg, A., Boutilier, K. (2011). Microarray-Based Identification of Transcription Factor Target Genes. In: Yuan, L., Perry, S. (eds) Plant Transcription Factors. Methods in Molecular Biology, vol 754. Humana Press. https://doi.org/10.1007/978-1-61779-154-3_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-154-3_7

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-153-6

  • Online ISBN: 978-1-61779-154-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation