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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Gene Regulation During Sporulation

Sporulation is a complex developmental process that allows certain Gram-positive bacteria, such as Bacillus subtilis and Clostridium species, to survive extreme environmental conditions. This process is tightly regulated by a series of signaling cascades and transcriptional controls, ensuring the formation of a highly resistant endospore.Sporulation is triggered by unfavorable conditions, such as nutrient depletion, and is governed by a phosphorelay system. One of the sensor kinases, such as...
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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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Related Experiment Video

Updated: Jul 14, 2026

Measuring Gene Expression in Bombarded Barley Aleurone Layers with Increased Throughput
10:29

Measuring Gene Expression in Bombarded Barley Aleurone Layers with Increased Throughput

Published on: March 30, 2018

Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley

Marc Strickert1, Nese Sreenivasulu, Björn Usadel

  • 1Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany. stricker@ipk-gatersleben.de

BMC Bioinformatics
|May 24, 2007
PubMed
Summary

High-throughput multidimensional scaling (HiT-MDS) visualizes gene expression in barley endosperm development. The refined HiT-MDS-2 method reveals functional relationships and validates gene expression patterns during grain development.

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Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling
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Related Experiment Videos

Last Updated: Jul 14, 2026

Measuring Gene Expression in Bombarded Barley Aleurone Layers with Increased Throughput
10:29

Measuring Gene Expression in Bombarded Barley Aleurone Layers with Increased Throughput

Published on: March 30, 2018

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling
07:18

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Published on: May 21, 2020

Area of Science:

  • Plant biology
  • Genomics
  • Bioinformatics

Background:

  • Micro- and macroarray technologies generate vast gene expression data during plant development.
  • Effective visualization is crucial for understanding gene expression patterns and coexpressed gene relationships.
  • Analyzing barley endosperm development provides insights into regulatory behavior and cellular responses.

Purpose of the Study:

  • To refine the high-throughput multidimensional scaling (HiT-MDS) method for analyzing gene expression data.
  • To assess the quality and reliability of gene expression patterns using HiT-MDS.
  • To derive functional relationships of coexpressed genes in developing barley endosperm.

Main Methods:

  • Application of a refined high-throughput multidimensional scaling (HiT-MDS-2) method.
  • Embedding temporal expression profiles of 4824 genes across 14 time points into 2D displays.
  • Utilizing a correlation-based similarity measure and power transformation of correlation terms.

Main Results:

  • Faithful 2D embedding of gene expression profiles, grouping coexpressed genes by expression pattern similarity.
  • A characteristic bipolar sandglass shape emerged, linked to distinct developmental phases (pre-storage, intermediate, storage).
  • Successful mapping of functional gene annotations to the visualization for identifying major functional categories.

Conclusions:

  • The HiT-MDS-2 method enhances global visualization of gene expression patterns.
  • It effectively validates gene expression centroids derived from clustering algorithms.
  • Facilitates easy localization of key functional categories within barley endosperm development data.