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MassBank: a public repository for sharing mass spectral data for life sciences.
TLDR
MassBank is the first public repository of mass spectra of small chemical compounds for life sciences and provides a merged spectrum for each compound prepared by merging the analyzed ESI-MS(2) data on an identical compound under different collision-induced dissociation conditions.
Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor.
TLDR
The functional genomics approach through the integration of metabolomics and transcriptomics presented here provides an innovative means of identifying novel gene functions involved in plant metabolism.
Effects of sulfur nutrition on expression of the soybean seed storage protein genes in transgenic petunia.
TLDR
Results indicate that this mechanism of gene regulation in response to sulfur nutrition is conserved in petunia even though it is not used to regulate its own major seed storage proteins.
Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis
TLDR
Two R2R3-Myb transcription factors are found that positively control the biosynthesis of GSLs in Arabidopsis thaliana by an integrated omics approach and a working model for regulation of GSL production involving these genes, renamed Production of Methionine-Derived Glucosinolate (PMG) 1 and 2 are postulated.
Global expression profiling of sulfur-starved Arabidopsis by DNA macroarray reveals the role of O-acetyl-l-serine as a general regulator of gene expression in response to sulfur nutrition.
TLDR
A positive correlation between the changes of expression levels by sulfur deficiency and by OAS treatment among the clones tested is revealed, suggesting that mRNA accumulation of a number of genes under sulfur deficiency is mainly controlled by Oas concentrations in tissues.
Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana.
TLDR
This is the first report of investigation for gene-to-metabolite networks regulating sulfur and nitrogen nutrition and secondary metabolism in Arabidopsis, with integration of metabolomics and transcriptomics, and specific responses to either sulfur or nitrogen deficiency were observed.
Coordinated activation of metabolic pathways for antioxidants and defence compounds by jasmonates and their roles in stress tolerance in Arabidopsis.
TLDR
The results suggest that the coordinated activation of the metabolic pathways mediated by jasmonates provides resistance to environmental stresses.
The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.
TLDR
Genome-wide transcriptional gene-to-gene correlations, analyzed by hierarchical cluster analysis (HCA), indicated that the data set is useful for identification of clusters of co-expressed genes, and to predict the functions of unknown genes, even if a gene's function is not directly related to the experiments included in AtGenExpress.
The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.
TLDR
Genome-wide transcriptional gene-to-gene correlations, analyzed by hierarchical cluster analysis (HCA), indicated that the data set is useful for identification of clusters of co-expressed genes, and to predict the functions of unknown genes, even if a gene's function is not directly related to the experiments included in AtGenExpress.
Elucidation of Gene-to-Gene and Metabolite-to-Gene Networks in Arabidopsis by Integration of Metabolomics and Transcriptomics*
TLDR
It is suggested that regulatory metabolites and transcriptional factor genes can be identified by this approach, based on the assumption that they cluster with the downstream genes they regulate.
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