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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...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...

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Related Experiment Video

Updated: Jun 1, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Relating protein adduction to gene expression changes: a systems approach.

Bing Zhang1, Zhiao Shi, Dexter T Duncan

  • 1Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. bing.zhang@vanderbilt.edu

Molecular Biosystems
|May 20, 2011
PubMed
Summary

This study introduces a systems approach to understand how protein damage from electrophiles like 4-hydroxy-2-nonenal (HNE) impacts human diseases, revealing new insights into cellular stress responses.

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Last Updated: Jun 1, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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Published on: October 19, 2021

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
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Published on: November 3, 2010

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12:29

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Published on: July 28, 2017

Area of Science:

  • Biochemistry and Molecular Biology
  • Systems Biology
  • Toxicology

Background:

  • Reactive electrophiles, such as 4-hydroxy-2-nonenal (HNE), modify proteins, contributing to oxidant-associated human diseases.
  • The mechanisms by which protein damage leads to adaptive effects and toxicity remain poorly understood.

Purpose of the Study:

  • To develop a systems biology approach for linking protein adduction to gene expression changes.
  • To identify novel protein damage sensors and their regulatory mechanisms.

Main Methods:

  • Integrated analysis of protein adduction, gene expression, protein-DNA, and protein-protein interaction data.
  • Utilized a random walk strategy to infer upstream signaling networks from transcription factors.
  • Overlaid protein adduction data onto inferred networks to predict stress sensors.

Main Results:

  • The developed workflow successfully rediscovered known mechanisms of electrophile stress.
  • Generated novel hypotheses regarding cellular sensors of protein damage.
  • Demonstrated the general applicability of the framework across 103 known pathways.

Conclusions:

  • The systems approach provides a powerful framework for analyzing protein modification data, including adduction and phosphoproteomics.
  • This method advances our understanding of cellular responses to oxidative stress and electrophile damage.
  • Facilitates the discovery of novel stress sensors and regulatory pathways in human diseases.