Source 1primary paper2010The Plant Genome
Toolkit/Microarray expression profiling
Microarray expression profiling
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Microarray expression profiling is a transcriptomic assay used in developing soybean (Glycine max) seeds to identify mRNAs under circadian clock control. In the cited study, it measured rhythmic transcript abundance, quantified the fraction of circadian-regulated mRNAs, and enabled comparison of expression phase and functional categories between seed and leaf tissues.
Usefulness & Problems
Why this is useful
This assay is useful for detecting circadian-regulated gene expression programs at transcriptome scale in a specific tissue. In the cited soybean seed study, it supported identification of rhythmic mRNAs, comparison of circadian phase between tissues, and association of rhythmic transcripts with functional categories such as protein synthesis, fatty acid metabolism, and photosynthesis.
Source:
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Problem solved
It addresses the problem of determining which mRNAs in developing soybean seeds are controlled by the circadian clock and how their temporal expression differs from other tissues. The study specifically used it to measure rhythmic expression and reveal that some circadian-regulated genes have different phases in seeds than in leaves from the same plants.
Problem links
Need precise spatiotemporal control with light input
DerivedMicroarray expression profiling is a transcriptomic assay used here to identify circadian clock-controlled mRNAs in developing soybean (Glycine max) seeds. In the cited study, it measured rhythmic gene expression and enabled comparison of circadian expression phase and functional categories between seed and leaf tissues.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete measurement method used to characterize an engineered system.
Mechanisms
comparative temporal expression profilingcomparative temporal expression profilingpromoter element enrichment analysispromoter element enrichment analysistranscript hybridization-based expression measurementtranscript hybridization-based expression measurementTechniques
Functional AssayTarget 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: sensor
The documented implementation is microarray-based transcript expression profiling performed on developing soybean seeds to identify circadian clock-controlled genes. The supplied evidence does not specify array platform, sampling interval, normalization workflow, promoter analysis pipeline, or any special cofactors or construct requirements.
The supplied evidence is limited to a single 2010 soybean seed study and does not provide performance metrics such as sensitivity, dynamic range, probe coverage, or validation by independent assays. The evidence also does not describe whether the observed rhythmic transcripts were independently confirmed beyond the microarray-based analysis.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
fraction of detected seed mRNAs with circadian expression 1.8 %
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Approval Evidence
1 source4 linked approval claimsfirst-pass slug microarray-expression-profiling
Microarray expression profiling was used to identify genes expressed in developing soybean ( Glycine max ) seeds that are controlled by the circadian clock.
Source:
comparative expression phasesupports
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
Source:
functional enrichmentsupports
Circadian-regulated genes in developing soybean seeds included genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis.
Source:
measurement resultsupports
In developing soybean seeds, 1.8% of detected mRNAs were expressed in a circadian rhythm.
Source:
promoter element enrichmentsupports
Known circadian and light-controlled promoter elements were over-represented in promoters of clock-controlled seed genes, and the over-represented elements varied according to circadian phase.
Source:
Comparisons
Source-backed strengths
The method provided transcriptome-wide detection of circadian-regulated mRNAs in developing soybean seeds and yielded a quantitative estimate that 1.8% of detected mRNAs were rhythmic. It also supported biologically informative comparisons across tissues and functional enrichment observations, including rhythmic genes linked to protein synthesis, fatty acid metabolism, and photosynthesis.
Source:
A subset of circadian-regulated genes showed different expression phases in developing seeds compared with leaves from the same plants.
Compared with native green gel system
Microarray expression profiling and native green gel system address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Compared with open-source microplate reader
Microarray expression profiling and open-source microplate reader address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Compared with plant transcriptome profiling
Microarray expression profiling and plant transcriptome profiling address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Ranked Citations
- 1.