The DOI matches its Crossref record; 67 of the 67 references it cites were found in a registry or an index.
Co‐expression tools for plant biology: opportunities for hypothesis generation and caveats
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 values, and the influence of data sets used for co‐expression analysis. Finally, examples from the literature will be presented, wherein co‐expression has been used to corroborate and discover various aspects of plant biology.
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Cites
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A gene expression map of Arabidopsis thaliana development
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Cited by
Effects of abiotic stress on plants: a systems biology perspective
Cramer, G. R., Urano, K., Delrot, S., Pezzotti, M., & Shinozaki, K. (2011) · BMC Plant Biology · doi:10.1186/1471-2229-11-163 · Cited by 1,375
Arabidopsis and primary photosynthetic metabolism – more than the icing on the cake
Stitt, M., Lunn, J., & Usadel, B. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2010.04142.x · Cited by 349
Self-citationAraújo, W. L., Ishizaki, K., Nunes-Nesi, A., Larson, T. R., Tohge, T., Krahnert, I., Witt, S., Obata, T., Schauer, N., Graham, I. A., et al. (2010) · The Plant Cell · doi:10.1105/tpc.110.075630 · Cited by 340
CYP716A Subfamily Members are Multifunctional Oxidases in Triterpenoid Biosynthesis
Fukushima, E. O., Seki, H., Ohyama, K., Ono, E., Umemoto, N., Mizutani, M., Saito, K., & Muranaka, T. (2011) · Plant and Cell Physiology · doi:10.1093/pcp/pcr146 · Cited by 309
Learning from Co-expression Networks: Possibilities and Challenges
Serin, E. A. R., Nijveen, H., Hilhorst, H. W. M., & Ligterink, W. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.00444 · Cited by 304
Metadata
- Authors
- USADEL, B., OBAYASHI, T., MUTWIL, M., GIORGI, F. M., BASSEL, G. W., TANIMOTO, M., CHOW, A., STEINHAUSER, D., PERSSON, S., & PROVART, N. J.
- Venue
- Plant, Cell & Environment
- Publisher
- Wiley
- Published
- 2009-11-05
- Volume
- 32
- Issue
- 12
- Pages
- 1633-1651
- ISSN
- 0140-7791 (ISSN-L)
- 1365-3040
- OpenAlex
- W1995869668
- Cited by
- 476
- References
- 67
- FWCI
- 11.28
- Type
- journal article
- Language
- en
- Open access
- closed
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- USADEL, B., OBAYASHI, T., MUTWIL, M., GIORGI, F. M., BASSEL, G. W., TANIMOTO, M., CHOW, A., STEINHAUSER, D., PERSSON, S., & PROVART, N. J. (2009). Co‐expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant, Cell & Environment. https://doi.org/10.1111/j.1365-3040.2009.02040.x
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