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.
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Claims 7
Claim · model-written summary
CressExpress computes correlations between query genes and other Arabidopsis genes.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianae0 - Outcome
- patterns of correlated expressione0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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.”
Claim · model-written summary
CressExpress enables tissue-specific coexpression networks using tissue-based input filtering, unlike other tools.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- tissue-specific coexpression networkse0
- Comparator
- other coexpression toolse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Unlike other coexpression tools, CressExpress allows characterization of tissue-specific coexpression networks through user-driven filtering of input data based on sample tissue type.”
t0“Arabidopsis”
Claim · model-written summary
CressExpress ranks candidate genes by connections shared with at least two query genes for pathway analysis.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- identification of novel candidatese0
- Value
- two or moree0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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.”
t0“Arabidopsis”
Claim · model-written summary
CressExpress returns complete results and settings through an emailed website link after web-based experiments.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- full complement of resultse0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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.”
t0“Arabidopsis”
Claim · model-written summary
CressExpress offers strictly versioned expression datasets from MAS5, GCRMA and RMA processing.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- expression data from MAS5, GCRMA, and RMA array processing algorithmse0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Data sets featured in CressExpress are strictly versioned and include expression data from MAS5, GCRMA, and RMA array processing algorithms.”
t0“Arabidopsis”
Claim · model-written summary
Subselecting samples produces a richer coexpression network for Arabidopsis flowering genes.
- Taxon
- ArabidopsisArabidopsise0
- Outcome
- network for genes involved in floweringe0
- Direction
- richere0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We show that subselecting sample types produces a richer network for genes involved in flowering in Arabidopsis.”
Claim · model-written summary
CressExpress provides URL-based direct expression access to assess query gene coexpression and prospective pathway-level information.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- direct access to expression valuese0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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.”
t0“Arabidopsis”