The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses.

By Kiana Toufighi, S. Brady, Ryan S. Austin, E. Ly, Nicholas J. Provart. The Plant Journal, 2005

766 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/11d7cf7937acc027992e34869bb7122d4696bf78

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Plant Science

Citations in the corpus

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function (2010, methodology): “We include linkouts to model organism databases (FlyBase, WormBase, SGD and TAIR) and to the Arabidopsis resource BAR (19) that is useful to plant users.”
Ornithine-δ-aminotransferase is essential for Arginine Catabolism but not for Proline Biosynthesis (2008, methodology): “Additional evidence against a direct entry of Orn-derived P5C into Pro biosynthesis was derived from public microarray-expression data analysed with the BAR e-northern web-tool [28,29].”
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology[OPEN] (2017, methodology): “It does this by calculating the correlation coef ﬁ cients for expression for all gene expression vectorscomparedwithanexpressionpatternthattheuserde ﬁ nes ortotheexpressionpatternassociatedwithasingleAGIIDorgene name that a user enters (Tou ﬁ ghi et al., 2005).”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “At the same time, the Bio-Array Resources for Plant Biology’s expression browser (Toufighi et al., 2005) was used to identify genes whose expression was enriched in the stem second-internode dataset.”
An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets (2007, methodology): “Also located on the bottom of the page are a variety of links to information on the gene(s), other BAR tools [10], and the XML source file.”
The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. (2007, methodology): “Other Web-based bioinformatics tools such as the “Expression Angler” or “Sample Angler” at BAR (Toufighi et al. 2005) can identify genes that respond similarly across samples (i.e., genes whose expression profiles are highly correlated), whereas HAYSTACK provides a model-based method for clustering…”
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis (2006, methodology): “The comprehensive systems-biology database (CSB. DB) (6), Botany Array Resource (BAR) (7), Arabidopsis Co-expression Tool (ACT) (8) and Genevestigator (9) provide co-expressed gene relationships calculated from the array data stored in TAIR and/or the NASCArrays.”
ATTED-II provides coexpressed gene networks for Arabidopsis (2008, background): “Although these databases provide similar information, each has unique functionalities that enhance the potential discovery of gene coexpression, such as cis element findings cooperated with coexpressed gene selection (10), combinatorial analyses using gene coexpression from multiple species (14), or”
The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. (2008, background): “The Botany Array Resource provides electronic Northerns (Toufighi et al., 2005), electronic fluorescent pictographs (Winter et al.”
Specific and coordinated control of indolic and aliphatic glucosinolate biosynthesis by R2R3-MYB transcription factors in Arabidopsis thaliana (2008, methodology): “However, co-expression studies using ExpressionAngler revealed a significant correlation of HIG1/MYB51 and HIG2/MYB122 expression in the AtGenExpress pathogen set (correlation coefficient r = 0.8; Toufighi et al. 2005).”
Approaches for extracting practical information from gene co-expression networks in plant biology. (2007, methodology): “…(http://www.arabidopsis.leeds. ac.uk/act/) (Jen et al. 2006), ATTED-II, Genevestigator (http://www.genevestigator.ethz.ch) (Zimmermann et al. 2004) and The Botany Array Resource (BAR) (http:// bbc.botany.utoronto.ca/) (Toufighi et al. 2005) are implemented with gene expression visualizing tools.”