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BIOINFORMATICS

CressExpress: A Tool For Large-Scale Mining of Expression Data from Arabidopsis^1,[W],[OA]

Section on Statistical Genetics, Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294 (V.S., G.P.P., T.M, I.C.); and University of North Carolina at Charlotte, Bioinformatics Research Center, North Carolina Research Campus, Kannapolis, North Carolina 28081 (A.E.L.)

CressExpress is a user-friendly, online, coexpression analysis tool for Arabidopsis (Arabidopsis thaliana) microarray expression data that computes patterns of correlated expression between user-entered query genes and the rest of the genes in the genome. Unlike other coexpression tools, CressExpress allows characterization of tissue-specific coexpression networks through user-driven filtering of input data based on sample tissue type. CressExpress also performs pathway-level coexpression analysis on each set of query genes, identifying and ranking genes based on their common connections with two or more query genes. This allows identification of novel candidates for involvement in common processes and functions represented by the query group. Users launch experiments using an easy-to-use Web-based interface and then receive the full complement of results, along with a record of tool settings and parameters, via an e-mail link to the CressExpress Web site. Data sets featured in CressExpress are strictly versioned and include expression data from MAS5, GCRMA, and RMA array processing algorithms. To demonstrate applications for CressExpress, we present coexpression analyses of cellulose synthase genes, indolic glucosinolate biosynthesis, and flowering. We show that subselecting sample types produces a richer network for genes involved in flowering in Arabidopsis. CressExpress provides direct access to expression values via an easy-to-use URL-based Web service, allowing users to determine quickly if their query genes are coexpressed with each other and likely to yield informative pathway-level coexpression results. The tool is available at http://www.cressexpress.org.

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: Ann E. Loraine (aloraine{at}uncc.edu).

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

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.107.115535

^* Corresponding author; e-mail aloraine{at}uncc.edu.

Received January 18, 2008; accepted April 29, 2008; published May 8, 2008.

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