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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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mRNA Stability and Gene Expression02:51

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The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
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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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Related Experiment Video

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Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells
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Pathway-level information extractor (PLIER) for gene expression data.

Weiguang Mao1,2, Elena Zaslavsky3, Boris M Hartmann3

  • 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.

Nature Methods
|June 29, 2019
PubMed
Summary
This summary is machine-generated.

Pathway-Level Information Extractor (PLIER) accurately infers biological insights from gene expression data. This method enhances cell proportion inference and identifies regulatory pathways, improving study replicability and trans-eQTL discovery.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Systems Biology

Background:

  • Accurate inference of biological insights from global gene expression studies is challenging.
  • Existing methods struggle with cell-type proportion and pathway activity inference.
  • Inter-study replicability remains a significant hurdle in gene expression analysis.

Purpose of the Study:

  • To introduce Pathway-Level Information Extractor (PLIER), a novel computational method for gene expression analysis.
  • To demonstrate PLIER's superiority over existing algorithms in inferring cell proportions and pathway activities.
  • To showcase PLIER's utility in improving inter-study replicability and identifying biological insights, including trans-eQTLs.

Main Methods:

  • Development of the Pathway-Level Information Extractor (PLIER) algorithm.
  • Benchmarking PLIER against existing cell proportion inference algorithms.
  • Application of PLIER to trans-eQTL identification and analysis of gene expression data.

Main Results:

  • PLIER significantly outperforms current methods for cell proportion inference.
  • PLIER effectively identifies specific pathways regulating gene expression.
  • The method demonstrates improved inter-study replicability in gene expression analyses.
  • PLIER facilitates novel biological insights in trans-eQTL studies.

Conclusions:

  • PLIER offers a broadly applicable and robust solution for extracting biological insights from gene expression data.
  • The method advances the field of gene expression analysis by improving accuracy and replicability.
  • PLIER is a valuable tool for researchers investigating cellular heterogeneity, pathway regulation, and genetic associations.