Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2006 Jul 1;34(Web Server issue):W504-9.
doi: 10.1093/nar/gkl204.

Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis

Iain W Manfield  1 , Chih-Hung Jen, John W Pinney, Ioannis Michalopoulos, James R Bradford, Philip M Gilmartin, David R Westhead
Affiliations

Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis

Iain W Manfield et al. Nucleic Acids Res. .

Abstract

The Arabidopsis Co-expression Tool, ACT, ranks the genes across a large microarray dataset according to how closely their expression follows the expression of a query gene. A database stores pre-calculated co-expression results for approximately 21,800 genes based on data from over 300 arrays. These results can be corroborated by calculation of co-expression results for user-defined sub-sets of arrays or experiments from the NASC/GARNet array dataset. Clique Finder (CF) identifies groups of genes which are consistently co-expressed with each other across a user-defined co-expression list. The parameters can be altered easily to adjust cluster size and the output examined for optimal inclusion of genes with known biological roles. Alternatively, a Scatter Plot tool displays the correlation coefficients for all genes against two user-selected queries on a scatter plot which can be useful for visual identification of clusters of genes with similar r-values. User-input groups of genes can be highlighted on the scatter plots. Inclusion of genes with known biology in sets of genes identified using CF and Scatter Plot tools allows inferences to be made about the roles of the other genes in the set and both tools can therefore be used to generate short lists of genes for further characterization. ACT is freely available at www.Arabidopsis.leeds.ac.uk/ACT.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Screen shot of a typical ACT output showing co-expression of genes encoding sub-units of the proteasome. Gene identifiers, correlation r-value, measures of statistical significance and annotation are shown.
Figure 2
Figure 2
The Clique Finder algorithm for identification of groups of consistently co-expressed genes.
Figure 3
Figure 3
Co-correlation Scatter Plot. The r-values for all genes against two queries, cca1 (266719_at) and lhy (261569_at), are displayed on a scatter plot. The values for all of the myb genes represented on the array are highlighted in red. The labelled genes are discussed in the text.
See this image and copyright information in PMC

References

    1. Craigon D.J., James N., Okyere J., Higgins J., Jotham J., May S. NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res. 2004;32:D575–D577. - PMC - PubMed
    1. Rhee S.Y., Beavis W., Berardini T.Z., Chen G.H., Dixon D., Doyle A., Garcia-Hernandez M., Huala E., Lander G., Montoya M., et al. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 2003;31:224–228. - PMC - PubMed
    1. Ball C.A., Awad I.A.B., Demeter J., Gollub J., Hebert J.M., Hernandez-Boussard T., Jin H., Matese J.C., Nitzberg M., Wymore F., et al. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res. 2005;33:D580–D582. - PMC - PubMed
    1. Toufighi K., Brady S.M., Austin R., Ly E., Provart N.J. The Botany Array Resource: e-Northerns, Expression Angling, and Promoter analyses. Plant J. 2005;43:153–163. - PubMed
    1. Zimmermann P., Hennig L., Gruissem W. Gene-expression analysis and network discovery using Genevestigator. Trends Plant Sci. 2005;10:407–409. - PubMed

Publication types

Substances