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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
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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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Mutation, Gene Flow, and Genetic Drift01:09

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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Deconvolution01:20

Deconvolution

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Deconvolution, also known as inverse filtering, is the process of extracting the impulse response from known input and output signals. This technique is vital in scenarios where the system's characteristics are unknown, and they must be inferred from the observable signals.
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Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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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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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
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GECO: gene expression correlation analysis after genetic algorithm-driven deconvolution.

Jamil Najafov1, Ayaz Najafov1

  • 1Department of Cell Biology, Harvard Medical School, Boston, MA, USA.

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|July 17, 2018
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Summary
This summary is machine-generated.

GECO software analyzes gene expression data to identify correlations and subpopulations. This aids in discovering mutation drivers and drug vulnerabilities within complex biological datasets.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Large-scale gene expression analysis is crucial for generating data-driven hypotheses.
  • Complex gene expression datasets often present challenges in extracting meaningful biological insights.

Purpose of the Study:

  • To develop GECO, a novel software for gene expression correlation analysis.
  • To enable the deconvolution of complex datasets into distinct subpopulations with correlated gene expression patterns.

Main Methods:

  • GECO employs a genetic algorithm-driven approach for deconvolution.
  • It performs mutational enrichment and pairwise drug sensitivity analyses.
  • A drug sensitivity screen function is integrated for subpopulation-specific drug effect identification.

Main Results:

  • GECO deconvolutes complex gene expression datasets into positively and negatively correlated subpopulations.
  • The software identifies mutational factors driving gene expression correlations.
  • Differential drug vulnerabilities and effective drugs for specific subpopulations are revealed.

Conclusions:

  • GECO provides a powerful tool for dissecting complex gene expression data.
  • It facilitates the identification of novel therapeutic targets and biomarkers.
  • The software enhances biological hypothesis generation from large-scale transcriptomic studies.