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

Abstract

SummaryThe Botany Array Resource provides the means for obtaining and archiving microarray data for Arabidopsis thaliana as well as biologist-friendly tools for viewing and mining both our own and other's data, for example, from the AtGenExpress Consortium. All the data produced are publicly available through the web interface of the database at http://bbc.botany.utoronto.ca. The database has been designed in accordance with the Minimum Information About a Microarray Experiment [Brazma, A., Hingamp, P., Quackenbush, J. et al. (2001) Minimum information about a microarray experiment (MIAME) -toward standards for microarray data. Nat. Genet. 29, 365] convention -all expression data are associated with the corresponding experimental details. The database is searchable and it also provides a set of useful and easy-to-use web-based data-mining tools for researchers with sophisticated yet understandable output graphics. These include Expression Browser for performing 'electronic Northerns', Expression Angler for identifying genes that are co-regulated with a gene of interest, and Promomer for identifying potential cis-elements in the promoters of individual or co-regulated genes.

A robust omics-based approach for the identification of glucosinolate biosynthetic genes

“…In contrast, thousands of transcriptome data available in the public databases have been obtained under a wide range of experimental conditions, and hence the higher similarity coefficient calculated on the basis of publicly available dataset indicates a constitutive or condition-independent coexpression relationship; that is, a set of genes with higher similarity are coexpressed across a variety of experimental conditions. Many coexpression analysis tools have been recently released, such as ATTED-II (the Arabidopsis thaliana trans-factor and cis-element prediction database) ), CSB.DB (the Comprehensive Systems-Biology Database) (Steinhauser et al 2004), BAR (the Botany Array Resource) (Toufighi et al 2005), ACT (the Arabidopsis Co-expression Tool) Manfield et al 2006), Genevestigator Zimmermann et al 2004), PED (Plant Gene Expression Database) (Horan et al 2008) and CressExpress (Srinivasasainagendra et al 2008). Some of these provide users the option of calculating the degree of similarity for a dataset.…”

Reduced activity ofArabidopsischromosome-cohesion regulator geneCTF7/ECO1alters cytosine methylation status and retrotransposon expression

“…With Gene Angler analysis, candidates have a Pearson correlation coefficient greater than the defined cut-off coefficient. 15 With the cutoff r D 0.65, we found several genes including DEFECTIVE IN MERISTEM SILENCING 11 (DMS11), DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1), and DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), all key genes involved in RNA-directed DNA methylation (RdDM). This process is unique to plants and is responsible for regulating gene silencing.…”

“…13 However, little is known about whether this gene has other roles, for example, transcriptional regulation, in which other ECO1 homologs are involved. 14 We used co-expression and bioinformatics analysis with Gene Angler (http://bbc.botany.utoronto.ca/ntools/cgi-bin/ ntools_expression_angler.cgi) 15 to determine whether Arabidopsis CTF7/ECO1 could affect the transcription of other genes. With Gene Angler analysis, candidates have a Pearson correlation coefficient greater than the defined cut-off coefficient.…”

Embryogenesis: Pattern Formation from a Single Cell

“…Two quasi-cell-typespecifi c gene expression data sets for embryo development have been generated by the Lindsey laboratory using laser capture microdissection, followed by RNA amplifi cation and hybridization to the Affymetrix ATH1 GeneChip (Casson et al, 2005;Spencer et al, 2007). These data sets encompass apical and basal regions of globular, heart and torpedo stage embryos, and are queryable for more than 22,000 genes on the ATH1 GeneChip using the eFP Browser of the Bio-Array Resource (Toufi ghi et al, 2005;Winter et al, 2007) or other online tools -except Genevestigator (Zimmermann et al, 2004), which removed these data sets because the amplifi cation procedure necessarily introduced biases towards the 3' probe sets, rendering expression signals (A) The SHR gene is expressed in the vascular cylinder (brown), but its activity is required for radial patterning in the adjacent cortex-endodermal initials (orange) and in the endodermis (yellow). SHR protein moves (arrows) to cells surrounding the vascular cylinder, where it induces the expression of SCR and, with the exception of the QC (red), other endodermis specifi c genes.…”