Transcriptomic analysis of wild type vs mpk3 mutants
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE34659 | GEO | 2012/01/31
SECONDARY ACCESSION(S): PRJNA151237
REPOSITORIES: GEO
Similar Datasets
Project description:au09-01_mpk mpk Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade. 2 dye-swap - wild type vs mutants
2012-01-31 | E-GEOD-34659 | biostudies-arrayexpress
Project description:au09-01_mpk_flagellin - wt-col0_flagellin Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade. Flagellin is a protein present in the flagellum of almost all bacteria and triggers Innate Immunity in plants, mediated by a MAPK phosphorylation signal cascade. To better understand the changes occuring in wt-Col0 flagellin treatment at the gene expression level, we would like to perform a microarray transcriptomic analysis. 1 dye-swap - treated vs untreated comparison
2012-01-31 | E-GEOD-34660 | biostudies-arrayexpress
Project description:au09-01_mpk_flagellin - wt-col0_flagellin Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade. Flagellin is a protein present in the flagellum of almost all bacteria and triggers Innate Immunity in plants, mediated by a MAPK phosphorylation signal cascade. To better understand the changes occuring in wt-Col0 flagellin treatment at the gene expression level, we would like to perform a microarray transcriptomic analysis.
2012-01-31 | GSE34660 | GEO
Project description:au08-06_mpk6_heat_stressed - au08-06_mpk6_heat_stressed - Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade. In previous studies, it was shown that the mpk6 KO mutant plants are significantly more tolerant to heat stress in comparison to wt and that after 3h treatment at 37°C, an activation of heat-shock proteins occures in the mpk6 mutant. To better understand the changes occuring in the mpk6 mutant upon heat stress at the gene expression level, we would like to perform a microarray transcriptomic analysis. - Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade. In previous studies, it was shown that the mpk6 KO mutant plants are significantly more tolerant to heat stress in comparison to wt and that after 3h treatment at 37°C, an activation of heat-shock proteins occures in the mpk6 mutant. To better understand the changes occuring in the mpk6 mutant upon heat stress at the gene expression level, we would like to perform a microarray transcriptomic analysis. Keywords: treated vs untreated comparison 4 dye-swap - CATMA arrays
2010-06-28 | E-GEOD-22568 | biostudies-arrayexpress
Project description:au08-06_mpk6_heat_stressed - au08-06_mpk6_heat_stressed - Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade. In previous studies, it was shown that the mpk6 KO mutant plants are significantly more tolerant to heat stress in comparison to wt and that after 3h treatment at 37°C, an activation of heat-shock proteins occures in the mpk6 mutant. To better understand the changes occuring in the mpk6 mutant upon heat stress at the gene expression level, we would like to perform a microarray transcriptomic analysis. - Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade. In previous studies, it was shown that the mpk6 KO mutant plants are significantly more tolerant to heat stress in comparison to wt and that after 3h treatment at 37°C, an activation of heat-shock proteins occures in the mpk6 mutant. To better understand the changes occuring in the mpk6 mutant upon heat stress at the gene expression level, we would like to perform a microarray transcriptomic analysis. Keywords: treated vs untreated comparison
2010-06-29 | GSE22568 | GEO
Project description:Huang1996 - Ultrasensitivity in MAPK cascade
The temporal sequence of kinase activation, from MAPKKK (activated RAF) to the final effector MAPK (activated ERK), is described here. It is observed from the model that there is an increase in sensitivity along the levels of the cascade, where the activity of MAPK reaches its maximal before MAPKKK.
This model is described in the article:
Ultrasensitivity in the mitogen-activated protein kinase cascade.
Huang CY, Ferrell JE Jr
Proc. Natl. Acad. Sci. U.S.A. 1996:93(19):10078-83
Abstract:
The mitogen-activated protein kinase (MAPK) cascade is a highly conserved series of three protein kinases implicated in diverse biological processes. Here we demonstrate that the cascade arrangement has unexpected consequences for the dynamics of MAPK signaling. We solved the rate equations for the cascade numerically and found that MAPK is predicted to behave like a highly cooperative enzyme, even though it was not assumed that any of the enzymes in the cascade were regulated cooperatively. Measurements of MAPK activation in Xenopus oocyte extracts confirmed this prediction. The stimulus/response curve of the MAPK was found to be as steep as that of a cooperative enzyme with a Hill coefficient of 4-5, well in excess of that of the classical allosteric protein hemoglobin. The shape of the MAPK stimulus/ response curve may make the cascade particularly appropriate for mediating processes like mitogenesis, cell fate induction, and oocyte maturation, where a cell switches from one discrete state to another.
The species K_PP_norm, KKK_P_norm and KK_PP_norm are the relative concentrations of the active MAPK, MAPKK and MAPKKK, that is the double, or single resp. phophorylated forms divided by the total concentrations of each kinase. For MAPK additionally the also active MAPK divided by the maximal concentration of active MAPK is given by rel_K_PP_max. The parameter K_PP_norm_max, the maximal ratio of active MapK, has to be calculated for each change of parameters.
This model is hosted on BioModels Database
and identified by: BIOMD0000000009
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
2005-02-10 | BIOMD0000000009 | BioModels
Project description:The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize.
2016-01-22 | GSE71377 | GEO
Project description:Pathak2013 - MAPK activation in response to various abiotic stresses
MAPK activation mechanism in response to various abiotic stress conditions, such as cold, salt, drought, H2O2, heavy metal and ethylene, in plants
This model is described in the article:
Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach.
Pathak RK, Taj G, Pandey D, Arora S, Kumar A.
Bioinformation 2013; 9(9): 443-449
Abstract:
Mitogen-Activated Protein Kinases (MAPKs) cascade plays an important role in regulating plant growth and development, generating cellular responses to the extracellular stimuli. MAPKs cascade mainly consist of three sub-families i.e. mitogen-activated protein kinase kinase kinase (MAPKKK), mitogen-activated protein kinase kinase (MAPKK) and mitogen activated protein kinase (MAPK), several cascades of which are activated by various abiotic and biotic stresses. In this work we have modeled the holistic molecular mechanisms essential to MAPKs activation in response to several abiotic and biotic stresses through a system biology approach and performed its simulation studies. As extent of abiotic and biotic stresses goes on increasing, the process of cell division, cell growth and cell differentiation slow down in time dependent manner. The models developed depict the combinatorial and multicomponent signaling triggered in response to several abiotic and biotic factors. These models can be used to predict behavior of cells in event of various stresses depending on their time and exposure through activation of complex signaling cascades.
This model is hosted on BioModels Database
and identified
by: BIOMD0000000491
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2013-11-15 | BIOMD0000000491 | BioModels
Project description:Pathak2013 - MAPK activation in response to various biotic stresses
MAPK activation mechanism in response to various biotic (fungal and bacterial pathogens) stress conditions in plants
This model is described in the article:
Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach.
Pathak RK, Taj G, Pandey D, Arora S, Kumar A.
Bioinformation 2013; 9(9): 443-449
Abstract:
Mitogen-Activated Protein Kinases (MAPKs) cascade plays an important role in regulating plant growth and development, generating cellular responses to the extracellular stimuli. MAPKs cascade mainly consist of three sub-families i.e. mitogen-activated protein kinase kinase kinase (MAPKKK), mitogen-activated protein kinase kinase (MAPKK) and mitogen activated protein kinase (MAPK), several cascades of which are activated by various abiotic and biotic stresses. In this work we have modeled the holistic molecular mechanisms essential to MAPKs activation in response to several abiotic and biotic stresses through a system biology approach and performed its simulation studies. As extent of abiotic and biotic stresses goes on increasing, the process of cell division, cell growth and cell differentiation slow down in time dependent manner. The models developed depict the combinatorial and multicomponent signaling triggered in response to several abiotic and biotic factors. These models can be used to predict behavior of cells in event of various stresses depending on their time and exposure through activation of complex signaling cascades.
This model is hosted on BioModels Database
and identified
by: BIOMD0000000492
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2013-11-15 | BIOMD0000000492 | BioModels
Project description:A unique allele of MAP kinase, mpk-1(ga111), displays a reversible, temperature-sensitive, tissue-specific defect in progression through meiotic prophase I. We performed gene expression profiling on mpk-1(ga111) animals at multiple times after shift to permissive temperature to identify candidate downstream effectors of MPK-1 signaling in the germline. This analysis delineated a cohort of genes whose expression requires MPK-1 (MAP kinase) signaling in germ cells in the pachytene stage of meiosis I. Keywords: Timecourse of C. elegans mpk-1 mutants
2006-08-01 | GSE5069 | GEO