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Published on May 8, 2008; 10.1104/pp.107.115535

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Received January 18, 2008
Accepted April 29, 2008

CressExpress: A tool for large-scale mining of expression data from Arabidopsis thaliana

Vinodh Srinivasasainagendra , Grier Page , Tapan Mehta , Issa Coulibaly , and Ann E. Loraine *

Section on Statistical Genetics, Department of Biostatistics, 1665 University Blvd., Ryals 327, University of Alabama at Birmingham, Birmingham, AL 35294; University of North Carolina at Charlotte, Bioinformatics Research Center, North Carolina Research Campus, 203 Oak Ave, Kannapolis, NC 28081

* Corresponding author; email: aloraine{at}uncc.edu.

CressExpress is a user-friendly, on-line co-expression analysis tool for Arabidopsis 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 co-expression tools, CressExpress allows characterization of tissue-specific co-expression networks through user-driven filtering of input data based on sample tissue type. CressExpress also performs Pathway-Level Co-expression (PLC) 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 email 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 co-expression analyses of cellulose synthase (CESA) genes, indolic glucosinolate biosynthesis, and flowering. We show that sub-selecting 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 co-expressed with each other and likely to yield informative PLC results. The tool is available at http://www.cressexpress.org.






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