ArticlePlant physiology2008
CressExpress: a tool for large-scale mining of expression data from Arabidopsis.
Article in Plant physiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 1 of them a synthesis that pooled it.
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Who cites it
56 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of the expression profiles of the Arabidopsis ESCRT machinery.Plant signaling & behavior · 2011Pooled it
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- Co-expression network analysis of protein phosphatase 2A (PP2A) genes with stress-responsive genes in Arabidopsis thaliana reveals 13 key regulators.Scientific reports · 2020Article
- Identification of gene expression logical invariants inPlant direct · 2019Article
- Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra.Tree physiology · 2018Article
- Gene coexpression network forPlant biotechnology (Tokyo, Japan) · 2017Article
- RapaNet: A Web Tool for the Co-Expression Analysis ofEvolutionary bioinformatics online · 2017Article
- petal: Co-expression network modelling in R.BMC systems biology · 2016Article
- Recent Advances in Understanding the Molecular Mechanisms Regulating the Root System Response to Phosphate Deficiency in Arabidopsis.Current genomics · 2016Article
- Learning from Co-expression Networks: Possibilities and Challenges.Frontiers in plant science · 2016Review
- Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis.PloS one · 2016Article
- Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods.EURASIP journal on bioinformatics & systems biology · 2015Article
- Phytosulfokine Regulates Growth in Arabidopsis through a Response Module at the Plasma Membrane That Includes CYCLIC NUCLEOTIDE-GATED CHANNEL17, H+-ATPase, and BAK1.The Plant cell · 2015Article
- Deep Sequencing Reveals the Effect of MeJA on Scutellarin Biosynthesis in Erigeron breviscapus.PloS one · 2015Article
- Article
- The PSI family of nuclear proteins is required for growth in arabidopsis.Plant molecular biology · 2014Article
- From dusk till dawn: the Arabidopsis thaliana sugar starving responsive network.Frontiers in plant science · 2014Article
- RiceFREND: a platform for retrieving coexpressed gene networks in rice.Nucleic acids research · 2013Article
- Genes and co-expression modules common to drought and bacterial stress responses in Arabidopsis and rice.PloS one · 2013Article
- Revealing the hidden relationship by sparse modules in complex networks with a large-scale analysis.PloS one · 2013Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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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