NASCArrays: a repository for microarray data generated by NASC's transcriptomics service

Craigon, David J.; James, N. I.; Okyere, John; Higgins, Janet; Jotham, Joan; May, Sean

doi:10.1093/nar/gkh133

Cited by 356 publications

(338 citation statements)

References 11 publications

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“…Using the Gene Atlas feature of the Genevestigator Web site (Zimmermann et al, 2004), which collates data from different microarray experiments (Edgar et al, 2002;Brazma et al, 2003;Craigon et al, 2004), the expression profile of these genes is largely similar to our northern data. One exception is ATHB27, for which we only see high levels of expression in open flowers, but is reported to be fairly ubiquitously expressed by Gene Atlas.…”

Section: The Arabidopsis Zf-hd Family Members Are All Expressed In Flmentioning

confidence: 58%

The Arabidopsis Zinc Finger-Homeodomain Genes Encode Proteins with Unique Biochemical Properties That Are Coordinately Expressed during Floral Development

2006

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Arabidopsis (Arabidopsis thaliana) contains approximately 100 homeobox genes, many of which have been shown to play critical roles in various developmental processes. Here we characterize the zinc finger-homeodomain (ZF-HD) subfamily of homeobox genes, consisting of 14 members in Arabidopsis. We demonstrate that the HDs of the ZF-HD proteins share some similarities with other known HDs in Arabidopsis, but they contain distinct features that cluster them as a unique class of plant HD-containing proteins. We have carried out mutational analyses to show that the noncanonical residues present in the HDs of this family of proteins are important for function. Yeast (Saccharomyces cerevisiae) two-hybrid matrix analyses of the ZF-HD proteins reveal that these proteins both homo-and heterodimerize, which may contribute to greater selectivity in DNA binding. These assays also show that most of these proteins do not contain an intrinsic activation domain, suggesting that interactions with other factors are required for transcriptional activation. We also show that the family members are all expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development. Furthermore, we have identified loss-of-function mutations for six of these genes that individually show no obvious phenotype, supporting the idea that the encoded proteins have common roles in floral development. Based on these results, we propose the ZF-HD gene family encodes a group of transcriptional regulators with unique biochemical activities that play overlapping regulatory roles in Arabidopsis floral development.

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Section: The Arabidopsis Zf-hd Family Members Are All Expressed In Flmentioning

confidence: 58%

The Arabidopsis Zinc Finger-Homeodomain Genes Encode Proteins with Unique Biochemical Properties That Are Coordinately Expressed during Floral Development

2006

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“…These data suggest the existence of a sugar dose-dependent inhibitory response of AKINb1 gene expression. They are strengthened by expression data from experiment 15 of Genevestigator, which indicated a 2.5-fold decrease of AKINb1 expression when seedlings were grown with Suc in the medium compared to medium without Suc (M. Campbell, NASCArrays; Craigon et al, 2004). However, when the same experiment was performed after 2.5 d in the dark, the repressive effect of sugar remained but was more variable.…”

Section: Akinb Genes Are Differently Regulated By Lightmentioning

confidence: 96%

β-Subunits of the SnRK1 Complexes Share a Common Ancestral Function Together with Expression and Function Specificities; Physical Interaction with Nitrate Reductase Specifically Occurs via AKINβ1-Subunit

et al. 2008

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The SNF1/AMPK/SnRK1 kinases are evolutionary conserved kinases involved in yeast, mammals, and plants in the control of energy balance. These heterotrimeric enzymes are composed of one a-type catalytic subunit and two g-and b-type regulatory subunits. In yeast it has been proposed that the b-type subunits regulate both the localization of the kinase complexes within the cell and the interaction of the kinases with their targets. In this work, we demonstrate that the three b-type subunits of Arabidopsis (Arabidopsis thaliana; AKINb1, AKINb2, and AKINb3) restore the growth phenotype of the yeast sip1Dsip2Dgal83D triple mutant, thus suggesting the conservation of an ancestral function. Expression analyses, using AKINb promoter:: b-glucuronidase transgenic lines, reveal different and specific patterns of expression for each subunit according to organs, developmental stages, and environmental conditions. Finally, our results show that the b-type subunits are involved in the specificity of interaction of the kinase with the cytosolic nitrate reductase. Together with previous cell-free phosphorylation data, they strongly support the proposal that nitrate reductase is a real target of SnRK1 in the physiological context. Altogether our data suggest the conservation of ancestral basic function(s) together with specialized functions for each b-type subunit in plants.

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“…DNA array data thus obtained are deposited in public databases. On the other hand, DNA array data has been systematically acquired by the AtGenExpress (Goda et al 2008;Kilian et al 2007;Schmid et al 2005) and NASCArrays (Craigon et al 2004) by using the same analytical platform, i.e., Affymetrix GeneChip microarray. This led to the development of secondary databases equipped with web-based coexpression analysis tools that help in calculating and storing the information regarding the level of similarity of gene expression patterns, and this information is made available to users.…”

Section: Introductionmentioning

confidence: 99%

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

Hirai

2008

Phytochem Rev

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Transcriptome coexpression analysis, which is based on a vast amount of transcriptome data obtained by using DNA arrays, has become a routine method for functional genomics studies in Arabidopsis. This analysis enables us to predict the function of genes on the basis of a simple assumption that a set of genes involved in a particular biological process can be coexpressed under the control of a shared regulatory system. Candidate genes involved in glucosinolate biosynthesis were successfully identified by this approach. In this review, the methodology of coexpression analysis is briefly described. The advantages and disadvantages of this analysis are also discussed in the context of its ability to predict gene functions involved in glucosinolate biosynthesis.

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NASCArrays: a repository for microarray data generated by NASC's transcriptomics service

Cited by 356 publications

References 11 publications

The Arabidopsis Zinc Finger-Homeodomain Genes Encode Proteins with Unique Biochemical Properties That Are Coordinately Expressed during Floral Development

The Arabidopsis Zinc Finger-Homeodomain Genes Encode Proteins with Unique Biochemical Properties That Are Coordinately Expressed during Floral Development

β-Subunits of the SnRK1 Complexes Share a Common Ancestral Function Together with Expression and Function Specificities; Physical Interaction with Nitrate Reductase Specifically Occurs via AKINβ1-Subunit

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

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