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Related Concept Videos

What is Gene Expression?01:36

What is Gene Expression?

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 processed and...
What is Gene Expression?01:42

What is Gene Expression?

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...
What is Gene Expression?01:42

What is Gene Expression?

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...
Constitutive and Regulated Gene Expression01:27

Constitutive and Regulated Gene Expression

Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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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An Optogenetic Method to Control and Analyze Gene Expression Patterns in Cell-to-cell Interactions
07:59

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Published on: March 22, 2018

Principal-oscillation-pattern analysis of gene expression.

Daifeng Wang1, Ari Arapostathis, Claus O Wilke

  • 1Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas, United States of America.

Plos One
|January 19, 2012
PubMed
Summary
This summary is machine-generated.

Principal Oscillation Pattern (POP) analysis is now applied to genome-wide gene expression data. This method effectively infers gene expression oscillation patterns, offering valuable insights into dynamic genomic systems.

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Area of Science:

  • Genomics
  • Computational Biology
  • Systems Biology

Background:

  • Principal Oscillation Pattern (POP) analysis is a robust technique for analyzing dynamic system characteristics from time-series data.
  • Genome-wide gene expression studies generate complex time-series datasets.
  • Direct estimation of genomic system matrices is often infeasible due to the high dimensionality (number of genes) relative to the number of time points.

Purpose of the Study:

  • To introduce and validate the application of Principal Oscillation Pattern (POP) analysis to genome-wide time-series gene-expression data.
  • To infer and characterize oscillation patterns within gene expression dynamics.
  • To address the challenge of estimating genomic system matrices in high-dimensional data.

Main Methods:

  • Singular Value Decomposition (SVD) was employed to identify significant eigengenes from the genomic data.
  • The eigen-genomic system, comprising key eigengenes, was analyzed using POP analysis.
  • The Principal Oscillation Patterns (POPs) of individual genes were inferred by leveraging the linear relationships between eigengenes and genes.

Main Results:

  • The study successfully applied POP analysis to both simulated and real-world genome-wide gene-expression datasets.
  • POP analysis demonstrated its applicability and effectiveness in inferring gene expression oscillation patterns.
  • The method provided results that favorably compared with experimental validation and existing computational approaches.

Conclusions:

  • Principal Oscillation Pattern (POP) analysis is a viable and powerful technique for uncovering dynamic patterns in genome-wide gene expression data.
  • This approach offers complementary information to existing methods, enhancing our understanding of complex genomic systems.
  • The study establishes POP analysis as a valuable tool for time-series genomic data analysis.