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MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Widespread changes in the expression of genes encoding receptor kinases, transcription factors, components of signalling pathways, proteins involved in post-translational modification and turnover, and proteins involved with the synthesis and sensing of cytokinins, abscisic acid and ethylene revealing large-scale rewiring of the regulatory network is an early response to sugar depletion are revealed.
PHO2, MicroRNA399, and PHR1 Define a Phosphate-Signaling Pathway in Plants1[W][OA]
- R. Bari, Bikram Datt Pant, M. Stitt, W. Scheible
- Biology, Environmental SciencePlant Physiology
- 5 May 2006
It is shown here that miR399 primary transcripts are also strongly induced by low Pi and rapidly repressed after addition of Pi, which placesmiR399 and PHO2 in a branch of the Pi-signaling network downstream of PHR1.
The interaction between elevated carbon dioxide and nitrogen nutrition: the physiological and molecular background
This review summarizes the numerous studies that have described the interaction between the nitrogen supply and the response of photosynthesis, metabolism and growth to elevated [CO2], and discusses emerging evidence that signals derived from nitrate and nitrogen metabolites such as glutamine act to regulate the expression of genes involved inNitrate and ammonium uptake and assimilation.
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
RobiNA is an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface and supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state of the art biostatistical methods developed in the R/Bioconductor projects.
Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses1
New developments are presented, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, and extensions of the software to incorporate more biological information including visualization of coresponding genes and horizontal searches for similar global responses across large numbers of arrays.
Genome-Wide Reprogramming of Primary and Secondary Metabolism, Protein Synthesis, Cellular Growth Processes, and the Regulatory Infrastructure of Arabidopsis in Response to Nitrogen1[w]
Transcriptome analysis revealed rapid responses in the expression of many genes potentially involved in regulation, including genes for trehalose metabolism and hormone metabolism, protein kinases and phosphatases, receptor kinases, and transcription factors.
A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize.
- B. Usadel, F. Poree, A. Nagel, M. Lohse, Angelika Czedik-Eysenberg, M. Stitt
- Environmental SciencePlant, cell & environment
- 1 September 2009
These analyses illustrate how MapMan can be used to analyse and compare global transcriptional responses between phylogenetically distant species, and show that analyses at the level of functional categories are especially useful in cross-species comparisons.
Rising Co2 Levels and Their Potential Significance for Carbon Flow in Photosynthetic Cells
- M. Stitt
- Environmental Science
- 1 October 1991
It is concluded that control is usually shared between Rubisco (which responds sensitively to CO2) and other components (which respond less sensitively), and that photosynthesis will be stimulated by 25–75% when the CO2 concentration is doubled from 35 to 70 Pa.
Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus.
Differentially expressed and highly P-specific putative regulator genes were identified that presumably play central roles in coordinating the complex responses of plants to changes in P nutrition.
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments
PageMan is introduced, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies, enabling researchers to gain a rapid overview of the biological responses in the experiments.