A gene expression map of Arabidopsis thaliana development


Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals1. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.

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Figure 1: Expressed genes, expression dynamics and marker genes.
Figure 2: Global expression trends.
Figure 3: Sliding-window analysis of coexpression and expression levels along chromosome I.
Figure 4: Expression levels of Gene Ontology categories and relationship between different measures of expression.
Figure 5: Coexpression of genes encoding protein complexes and gene families.

Change history

  • 23 May 2005

    Replaced Table 4

  • 02 June 2005

    Replaced Table 2


  1. 1.

    NOTES: In the version of Supplementary Table 4 online that originally accompanied this article, the number of gene families appeared smaller than was truly the case. This error has been corrected online.

  2. 2.

    NOTES: In the version of Supplementary Table 2 online that originally accompanied this article, the values for the A/C pairs were incorrect. This error has been corrected online.


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We thank F. Mehrtens, B. Weisshaar, R. Heidstra, B. Scheres, M. Yoshikawa, S. Poethig, D. Twell and the CAGE consortium (M. Kuiper, M. Vuylsteke, J.P. Renou, F. Bitton and M. Luijten) for providing RNA samples; P. Benfey and A. Zien for discussion; and K. Bomblies, R. Clark and A. Maizel for comments on the manuscript. This work was supported by the Deutsche Forschungsgemeinschaft through a grant to L. Nover, T. Altmann and D.W. and by the Max Planck Society. D.W. is a director of the Max Planck Institute.

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Correspondence to Detlef Weigel.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Assessment of replicate quality for 79 samples probed in triplicate. (PDF 519 kb)

Supplementary Fig. 2

Examples of gene expression profiles. (PDF 911 kb)

Supplementary Fig. 3

Principal Component Analysis of entire organs and tissues and sorted root cells. (PDF 418 kb)

Supplementary Fig. 4

Fraction of genes detected in each sample. (PDF 1083 kb)

Supplementary Fig. 5

Sliding-window analysis of co-expression along each chromosome. (PDF 1235 kb)

Supplementary Fig. 6

Sliding-window analysis of co-expression using different window sizes. (PDF 1223 kb)

Supplementary Fig. 7

Genes encoding the PF02713 (DUF220) protein domain form a hot-spot of co-expression on chromosome I. (PDF 1003 kb)

Supplementary Fig. 8

Sliding window analysis of averaged expression levels along each chromosome. (PDF 796 kb)

Supplementary Fig. 9

Extent of correlated expression among duplicated genes. (PDF 1042 kb)

Supplementary Fig. 10

Hierarchical clustering of genes encoding WRKY and MADS domain transcription factors. (PDF 1555 kb)

Supplementary Table 1

Sample descriptions and growth conditions. (PDF 64 kb)

Supplementary Table 2

Summary statistics of replicate quality. (PDF 53 kb)

Supplementary Table 3

Significance of differences in combined expression levels along each chromosome. (PDF 41 kb)

Supplementary Table 4

Coexpression of gene families. (PDF 84 kb)

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Schmid, M., Davison, T., Henz, S. et al. A gene expression map of Arabidopsis thaliana development. Nat Genet 37, 501–506 (2005) doi:10.1038/ng1543

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