Source 1primary paper2007The Plant Journal
Toolkit/model bioinformatics analysis
model bioinformatics analysis
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Model bioinformatics analysis in this context is a computation-based analysis of Arabidopsis thaliana transcript expression responses to UV-B light, drought, and cold stress using the AtGenExpress global stress dataset. It interprets stress-responsive gene expression patterns across multiple abiotic conditions measured with the Affymetrix ATH1 microarray under standardized parallel protocols.
Usefulness & Problems
Why this is useful
This analysis is useful for identifying transcriptomic responses shared across distinct abiotic stresses in Arabidopsis thaliana. The source literature indicates that it supports interpretation of a possible core environmental stress response gene set and the role of systemic signals in coordinating stress responses.
Source:
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
Source:
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
Problem solved
It addresses the problem of comparing genome-scale transcriptional responses across multiple abiotic stress conditions generated in a standardized experimental framework. In this study, the analysis was applied to UV-B light, drought, and cold stress to extract biological interpretations from the AtGenExpress global stress expression dataset.
Source:
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
Source:
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
Problem links
Need precise spatiotemporal control with light input
DerivedModel bioinformatics analysis in this context refers to analysis of Arabidopsis thaliana transcript expression responses to UV-B light, drought, and cold stress using the AtGenExpress global stress dataset. It is a computation-based resource for interpreting stress-responsive gene expression patterns across multiple abiotic conditions.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
cross-condition comparative analysiscross-condition comparative analysistranscriptomic pattern analysistranscriptomic pattern analysisTechniques
Computational DesignTarget processes
No target processes tagged yet.
Input: Light
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementoperating role: builder
The analysis is based on Arabidopsis thaliana transcript expression data generated with the Affymetrix ATH1 microarray. The reported application covers responses to UV-B light, drought, and cold stress using the AtGenExpress global stress dataset produced with standardized parallel protocols.
The supplied evidence supports only a general model bioinformatics analysis of transcript expression and does not specify algorithms, statistical models, normalization procedures, or predictive performance. Validation is limited here to interpretations from one Arabidopsis dataset and one publication.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Systemic signals generated by stressed tissue may play a major role in coordinating and executing stress responses.
there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses
Systemic signals generated by stressed tissue may play a major role in coordinating and executing stress responses.
there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses
Systemic signals generated by stressed tissue may play a major role in coordinating and executing stress responses.
there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses
Systemic signals generated by stressed tissue may play a major role in coordinating and executing stress responses.
there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses
Systemic signals generated by stressed tissue may play a major role in coordinating and executing stress responses.
there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses
Systemic signals generated by stressed tissue may play a major role in coordinating and executing stress responses.
there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses
Systemic signals generated by stressed tissue may play a major role in coordinating and executing stress responses.
there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses
Systemic signals generated by stressed tissue may play a major role in coordinating and executing stress responses.
there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses
Systemic signals generated by stressed tissue may play a major role in coordinating and executing stress responses.
there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses
Systemic signals generated by stressed tissue may play a major role in coordinating and executing stress responses.
there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses
The initial transcriptional stress reaction of Arabidopsis may include a core set of environmental stress response genes that function across multiple stress responses by adjusting energy balance.
Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
The initial transcriptional stress reaction of Arabidopsis may include a core set of environmental stress response genes that function across multiple stress responses by adjusting energy balance.
Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
The initial transcriptional stress reaction of Arabidopsis may include a core set of environmental stress response genes that function across multiple stress responses by adjusting energy balance.
Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
The initial transcriptional stress reaction of Arabidopsis may include a core set of environmental stress response genes that function across multiple stress responses by adjusting energy balance.
Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
The initial transcriptional stress reaction of Arabidopsis may include a core set of environmental stress response genes that function across multiple stress responses by adjusting energy balance.
Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
The initial transcriptional stress reaction of Arabidopsis may include a core set of environmental stress response genes that function across multiple stress responses by adjusting energy balance.
Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
The initial transcriptional stress reaction of Arabidopsis may include a core set of environmental stress response genes that function across multiple stress responses by adjusting energy balance.
Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
The initial transcriptional stress reaction of Arabidopsis may include a core set of environmental stress response genes that function across multiple stress responses by adjusting energy balance.
Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
The initial transcriptional stress reaction of Arabidopsis may include a core set of environmental stress response genes that function across multiple stress responses by adjusting energy balance.
Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
The initial transcriptional stress reaction of Arabidopsis may include a core set of environmental stress response genes that function across multiple stress responses by adjusting energy balance.
Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses.
This study reports a comprehensive Arabidopsis thaliana genome transcript expression dataset generated with the Affymetrix ATH1 microarray under multiple abiotic stress conditions using standardized parallel protocols.
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
This study reports a comprehensive Arabidopsis thaliana genome transcript expression dataset generated with the Affymetrix ATH1 microarray under multiple abiotic stress conditions using standardized parallel protocols.
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
This study reports a comprehensive Arabidopsis thaliana genome transcript expression dataset generated with the Affymetrix ATH1 microarray under multiple abiotic stress conditions using standardized parallel protocols.
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
This study reports a comprehensive Arabidopsis thaliana genome transcript expression dataset generated with the Affymetrix ATH1 microarray under multiple abiotic stress conditions using standardized parallel protocols.
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
This study reports a comprehensive Arabidopsis thaliana genome transcript expression dataset generated with the Affymetrix ATH1 microarray under multiple abiotic stress conditions using standardized parallel protocols.
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
This study reports a comprehensive Arabidopsis thaliana genome transcript expression dataset generated with the Affymetrix ATH1 microarray under multiple abiotic stress conditions using standardized parallel protocols.
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
This study reports a comprehensive Arabidopsis thaliana genome transcript expression dataset generated with the Affymetrix ATH1 microarray under multiple abiotic stress conditions using standardized parallel protocols.
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
This study reports a comprehensive Arabidopsis thaliana genome transcript expression dataset generated with the Affymetrix ATH1 microarray under multiple abiotic stress conditions using standardized parallel protocols.
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
This study reports a comprehensive Arabidopsis thaliana genome transcript expression dataset generated with the Affymetrix ATH1 microarray under multiple abiotic stress conditions using standardized parallel protocols.
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
This study reports a comprehensive Arabidopsis thaliana genome transcript expression dataset generated with the Affymetrix ATH1 microarray under multiple abiotic stress conditions using standardized parallel protocols.
a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray... Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols.
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
Approval Evidence
1 source1 linked approval claimfirst-pass slug model-bioinformatics-analysis
the results of a model bioinformatics analysis of gene expression in response to UV-B light, drought and cold stress
Source:
resource valuesupports
The reported dataset is presented as a prime reference resource for subsequent research into plant abiotic stress.
the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress
Source:
Comparisons
Source-backed strengths
A key strength is that the underlying dataset is described as comprehensive, genome-scale, and generated under multiple abiotic stress conditions with standardized parallel protocols. The analysis enabled cross-condition biological inferences, including a proposed core set of environmental stress response genes and a role for systemic signaling in stress coordination.
model bioinformatics analysis and Computational methods for LOV-based optogenetic tool development address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Compared with mathematical model of light-induced expression kinetics
model bioinformatics analysis and mathematical model of light-induced expression kinetics address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Compared with molecular dynamics simulations
model bioinformatics analysis and molecular dynamics simulations address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Relative tradeoffs: appears more independently replicated; looks easier to implement in practice.
Ranked Citations
- 1.