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. 2008 Jul;147(3):1004-16.
doi: 10.1104/pp.107.115535. Epub 2008 May 8.

CressExpress: A Tool for Large-Scale Mining of Expression Data From Arabidopsis

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Free PMC article

CressExpress: A Tool for Large-Scale Mining of Expression Data From Arabidopsis

Vinodh Srinivasasainagendra et al. Plant Physiol. .
Free PMC article

Abstract

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.

Figures

Figure 1.
Figure 1.
Two highly coexpressed genes from Arabidopsis. RMA-normalized expression values for AtST5a (AT1G74100; x axis) and CYP83B1 (y axis) are plotted relative to each other. Each point indicates expression values from a single array. Regressing expression values for CYP83B1 (y axis) against expression values for AtST5a (x axis) yields an r2 value of approximately 0.7, equivalent to Pearson's correlation coefficient of 0.85. The regression line appears as a dashed line on the plot.
Figure 2.
Figure 2.
CressExpress operation. Screen captures showing step-by-step operation of the coexpression tool are shown.
Figure 3.
Figure 3.
Distribution of KS-D test statistics for CressExpress data releases. KS-D statistics for release 2.0 (A), 3.0 (B), 3.1 (C), and 3.2 (D) are shown.
Figure 4.
Figure 4.
Coexpression network for flowering-related genes without (A) and with (B) sample-type filtering. In B, only samples derived from flowers were included in the analysis.
Figure 5.
Figure 5.
Cytoscape visualization depicting PLC results for CESA genes involved in primary(A) and secondary (B) cell wall biosynthesis.

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