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Plant Physiology 141:1219-1232 (2006)
© 2006 American Society of Plant Biologists

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BIOINFORMATICS

Consensus by Democracy. Using Meta-Analyses of Microarray and Genomic Data to Model the Cold Acclimation Signaling Pathway in Arabidopsis1,[W]

Catherine Benedict*, Matt Geisler, Johan Trygg, Norman Huner and Vaughan Hurry

Umeå Plant Science Centre, Department of Plant Physiology (C.B., M.G., V.H.) and Research Group of Chemometrics, Department of Chemistry (J.T.), Umeå University, S–901 87 Umea, Sweden; and Department of Biology and Biotron, University of Western Ontario, London, Ontario, Canada N6A 5B7 (N.H.)

The whole-genome response of Arabidopsis (Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a cis-element found in its promoter conferred induction (+1), repression (–1), or no transcriptional change (0) during cold stress. By statistically comparing these election results with the voting behavior of all genes on the same gene chip, we verified the bioactivity of novel cis-elements and defined whether they were inductive or repressive. Using in silico mutagenesis we identified functional binding consensus variants for the transcription factors studied. Our results suggest that the previously identified ICEr1 (induction of CBF expression region 1) consensus does not correlate with cold gene induction, while the ICEr3/ICEr4 consensuses identified using our algorithms are present in regulons of genes that were induced coordinate with observed ICE1 transcript accumulation and temporally preceding genes containing the dehydration response element. Statistical analysis of overlap and cis-element enrichment in the ICE1, CBF2, ZAT12, HOS9, and PHYA regulons enabled us to construct a regulatory network supported by multiple lines of evidence that can be used for future hypothesis testing.

1 This work was supported by grants from the Swedish Forestry and Agricultural Research Council (to V.H.).

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Catherine Benedict (catherine.benedict{at}plantphys.umu.se).

[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.106.083527.

* Corresponding author; e-mail catherine.benedict{at}plantphys.umu.se; fax 46–90–786–676.

Received May 12, 2006; returned for revision May 12, 2006; accepted June 2, 2006.




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