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Related Concept Videos

What is Gene Expression?01:42

What is Gene Expression?

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Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
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What is Gene Expression?01:36

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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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DNA Microarrays

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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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Cell Specific Gene Expression01:58

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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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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
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Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR
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Using a gene expression biomarker to identify DNA damage-inducing agents in microarray profiles.

J Christopher Corton1, Andrew Williams2, Carole L Yauk2

  • 1Integrated Systems Toxicology Division, NHEERL, US-EPA, Research Triangle Park, North Carolina.

Environmental and Molecular Mutagenesis
|October 18, 2018
PubMed
Summary
This summary is machine-generated.

The TGx-DDI biomarker accurately identifies chemicals that induce DNA damage (DDI) using the Running Fisher test. This transcriptomic biomarker shows high accuracy across different cell types and technologies for regulatory testing.

Keywords:
HepaRG cellsTK6 cellsbiomarkergene expression profilinggenotoxicitytoxicogenomics

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Area of Science:

  • Toxicology
  • Genomics
  • Biomarker Development

Background:

  • High-throughput transcriptomics are vital for in vitro screening of environmental chemicals.
  • The TGx-DDI biomarker (64-gene expression profile) predicts DNA damage-inducing (DDI) potential.
  • The utility of this biomarker with alternative computational methods requires further investigation.

Purpose of the Study:

  • To evaluate the accuracy of the TGx-DDI biomarker using the Running Fisher test for identifying DDI agents.
  • To assess the biomarker's performance across different cell lines and gene expression technologies.

Main Methods:

  • The TGx-DDI biomarker was tested using the Running Fisher nonparametric correlation test.
  • Experiments were conducted in human TK6 cells, HepaRG, HepG2, and embryonic stem cell-derived hepatocytes.
  • Gene expression data were analyzed using both microarray and nCounter technologies.

Main Results:

  • The Running Fisher test achieved balanced accuracies of 87-97% in TK6 cells for differentiating DDI and non-DDI compounds.
  • Accurate identification of DDI agents was observed in HepaRG cells (90%) but varied in other cell types.
  • The biomarker maintained high accuracy (89%) when using nCounter technology for gene expression profiling.

Conclusions:

  • The TGx-DDI biomarker, when analyzed with the Running Fisher test, effectively classifies DDI agents.
  • The study confirms the biomarker's utility and adaptability across various experimental conditions.
  • Findings support the use of this transcriptomic biomarker in regulatory chemical screening.