Journal article
Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats
B Usadel, T Obayashi, M Mutwil, FM Giorgi, GW Bassel, M Tanimoto, A Chow, D Steinhauser, S Persson, NJ Provart
Plant Cell and Environment | WILEY | Published : 2009
Abstract
Gene co-expression analysis has emerged in the past 5 years as a powerful tool for gene function prediction. In essence, co-expression analysis asks the question 'what are the genes that are co-expressed, that is, those that show similar expression profiles across many experiments, with my gene of interest?'. Genes that are highly co-expressed may be involved in the biological process or processes of the query gene. This review describes the tools that are available for performing such analyses, how each of these perform, and also discusses statistical issues including how normalization of gene expression data can influence co-expression results, calculation of co-expression scores and P val..
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Funding Acknowledgements
The authors wish to thank the developers of the co-expression tools and databases listed in Table 1 for helpful input towards its creation, and Wei Keat Lim and Andrea Califano, from Columbia University, for the CEL file randomization script used to perform the analysis shown in Fig. 6. We are also grateful to Steven Chatfield for proofreading and helpful comments. M. Tanimoto was supported through an NSERC grant to Joseph Colasanti at the University of Guelph. N. J. Provart is supported by a grant from NSERC. S. Persson and M. Mutwil are financially supported by the Max-Planck Gesellschaft.