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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...
Reporter Genes02:11

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
Commonly used reporter...
Gene Therapy00:59

Gene Therapy

Gene therapy is a technique where a gene is inserted into a person’s cells to prevent or treat a serious disease. The added gene may be a healthy version of the gene that is mutated in the patient, or it could be a different gene that inactivates or compensates for the patient’s disease-causing gene. For example, in patients with severe combined immunodeficiency (SCID) due to a mutation in the gene for the enzyme adenosine deaminase, a functioning version of the gene can be inserted. The...

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Related Experiment Video

Updated: May 30, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

NETGEM: Network Embedded Temporal GEnerative Model for gene expression data.

Vinay Jethava1, Chiranjib Bhattacharyya, Devdatt Dubhashi

  • 1Department of Computer Science and Engineering, Chalmers University ofTechnology, Göteborg, Sweden.

BMC Bioinformatics
|August 10, 2011
PubMed
Summary
This summary is machine-generated.

NETGEM models dynamic protein interactions from gene expression data. This new method identifies time-sensitive interactions and their functional roles, advancing our understanding of gene regulation.

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Genomics

Background:

  • Temporal gene expression analysis often overlooks network constraints and dynamic interactions.
  • Existing methods lack systematic approaches to link gene expression changes to interaction dynamics.
  • Understanding interaction dynamics is crucial for discovering regulatory mechanisms and perturbation effects.

Purpose of the Study:

  • To develop a model for analyzing protein interaction dynamics based on gene expression changes over time.
  • To systematically relate temporal gene expression data to the dynamics of underlying gene and protein interactions.

Main Methods:

  • Introduced NETGEM, a model based on Markov dynamics to infer interaction dynamics.
  • Treated interaction strengths as random variables modulated by priors, suitable for small sample sizes.
  • Developed a linear-time algorithm for efficient inference.

Main Results:

  • NETGEM successfully identified temporal interactions and their strengths from gene expression data.
  • The model determined functional categories of actively interacting protein partners.
  • NETGEM captured the dynamics of interactions in perturbed biological networks.

Conclusions:

  • NETGEM offers an effective balance between model complexity and data requirements.
  • The model can deduce actively interacting genes and their functional roles using temporal expression data.
  • NETGEM's ability to incorporate perturbed network information and its minimal input requirements suggest broad applicability.