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Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes

(2009) Plant Journal. 57(1). p.184-194
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Abstract
The Affymetrix ATH1 array provides a robust standard tool for transcriptome analysis, but unfortunately does not represent all of the transcribed genes in Arabidopsis thaliana. Recently, Affymetrix has introduced its Arabidopsis Tiling 1.0R array, which offers whole-genome coverage of the sequenced Col-0 reference strain. Here, we present an approach to exploit this platform for quantitative mRNA expression analysis, and compare the results with those obtained using ATH1 arrays. We also propose a method for selecting unique tiling probes for each annotated gene or transcript in the most current genome annotation, TAIR7, generating Chip Definition Files for the Tiling 1.0R array. As a test case, we compared the transcriptome of wild-type plants with that of transgenic plants overproducing the heterodimeric E2Fa-DPa transcription factor. We show that with the appropriate data pre-processing, the estimated changes per gene for those with significantly different expression levels is very similar for the two array types. With the tiling arrays we could identify 368 new E2F-regulated genes, with a large fraction including an E2F motif in the promoter. The latter groups increase the number of excellent candidates for new, direct E2F targets by almost twofold, from 181 to 334.
Keywords
Arabidopsis, expression analysis, Tiling array, ATH1 array, E2F, cell cycle

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Please use this url to cite or link to this publication:

Chicago
Naouar, Naïra, Klaas Vandepoele, Tim Lammens, Tineke Casneuf, Georg Zeller, Paul Van Hummelen, Detlef Weigel, et al. 2009. “Quantitative RNA Expression Analysis with Affymetrix Tiling 1.0R Arrays Identifies New E2F Target Genes.” Plant Journal 57 (1): 184–194.
APA
Naouar, N., Vandepoele, K., Lammens, T., Casneuf, T., Zeller, G., Van Hummelen, P., Weigel, D., et al. (2009). Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant Journal, 57(1), 184–194.
Vancouver
1.
Naouar N, Vandepoele K, Lammens T, Casneuf T, Zeller G, Van Hummelen P, et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant Journal. 2009;57(1):184–94.
MLA
Naouar, Naïra, Klaas Vandepoele, Tim Lammens, et al. “Quantitative RNA Expression Analysis with Affymetrix Tiling 1.0R Arrays Identifies New E2F Target Genes.” Plant Journal 57.1 (2009): 184–194. Print.
@article{528468,
  abstract     = {The Affymetrix ATH1 array provides a robust standard tool for transcriptome analysis, but unfortunately does not represent all of the transcribed genes in Arabidopsis thaliana. Recently, Affymetrix has introduced its Arabidopsis Tiling 1.0R array, which offers whole-genome coverage of the sequenced Col-0 reference strain. Here, we present an approach to exploit this platform for quantitative mRNA expression analysis, and compare the results with those obtained using ATH1 arrays. We also propose a method for selecting unique tiling probes for each annotated gene or transcript in the most current genome annotation, TAIR7, generating Chip Definition Files for the Tiling 1.0R array. As a test case, we compared the transcriptome of wild-type plants with that of transgenic plants overproducing the heterodimeric E2Fa-DPa transcription factor. We show that with the appropriate data pre-processing, the estimated changes per gene for those with significantly different expression levels is very similar for the two array types. With the tiling arrays we could identify 368 new E2F-regulated genes, with a large fraction including an E2F motif in the promoter. The latter groups increase the number of excellent candidates for new, direct E2F targets by almost twofold, from 181 to 334.},
  author       = {Naouar, Na{\"i}ra and Vandepoele, Klaas and Lammens, Tim and Casneuf, Tineke and Zeller, Georg and Van Hummelen, Paul and Weigel, Detlef and R{\"a}tsch, Gunnar and Inz{\'e}, Dirk and Kuiper, Martin and De Veylder, Lieven and Vuylsteke, Marnik},
  issn         = {0960-7412},
  journal      = {Plant Journal},
  keyword      = {Arabidopsis,expression analysis,Tiling array,ATH1 array,E2F,cell cycle},
  language     = {eng},
  number       = {1},
  pages        = {184--194},
  title        = {Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes},
  url          = {http://dx.doi.org/10.1111/j.1365-313X.2008.03662.x},
  volume       = {57},
  year         = {2009},
}

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