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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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?01:36

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...

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Related Experiment Video

Updated: May 27, 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

Integration of gene expression data with prior knowledge for network analysis and validation.

Michael Ante1, Edgar Wingender, Mathias Fuchs

  • 1Department of Bioinformatics, Medical School, Georg-August-University Goettingen, Goldschmidtstr, 1, 37077 Goettingen, Germany. m.ante@bioinf.med.uni-goettingen.de.

BMC Research Notes
|November 30, 2011
PubMed
Summary

This study integrates protein-protein interaction and metabolic networks with breast cancer expression data to identify key biological pathways. The analysis highlights the spindle checkpoint

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Area of Science:

  • Systems biology and bioinformatics
  • Computational biology and network analysis

Background:

  • Reconstructing biological networks from expression data often relies on in silico predictions or unspecific knowledge bases.
  • Existing methods struggle to accurately represent in vivo interactions and experimental expression data simultaneously.

Purpose of the Study:

  • To construct and validate biological networks (signaling and metabolic) that closely reflect in vivo interactions and experimental expression data.
  • To identify functional modules and key nodes within these networks for biological insight and potential drug target discovery.

Main Methods:

  • Filtered signaling (TRANSPATH) and metabolic (KEGG LIGAND) networks onto breast cancer SAGE expression data.
  • Applied varying levels of restrictiveness for edge and vertex selection.
  • Utilized pathway over-representation tests with refined null models for validation and functional module recovery.

Main Results:

  • Successfully integrated diverse network data with expression profiles, revealing the significant role of spindle checkpoint pathways in breast cancer.
  • Identified high-ranking key nodes that cluster into functionally relevant groups, confirmed by literature.
  • Demonstrated consistency across functional, topological, signaling, and metabolic analyses.

Conclusions:

  • Network construction required adaptation to mammalian protein identifiers and reaction-based metabolic semantics, necessitating validation.
  • Validation, though challenging, provided crucial biological insights and assessed network coherence despite fragmented data.
  • Key node analysis identified potential protein targets for drug discovery.