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Related Concept Videos

Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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,...
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Amplifying Signals via Enzymatic Cascade01:22

Amplifying Signals via Enzymatic Cascade

When a ligand binds to a cell-surface receptor, the receptor's intracellular domain changes shape, which may either activate its enzyme function or allow its binding to other molecules. The initial signal is amplified by most signal transduction pathways. This means that a single ligand molecule can activate multiple molecules of a downstream target. Proteins that relay a signal are most commonly phosphorylated at one or more sites, activating or inactivating the protein. Kinases catalyze the...
Intracellular Signaling Cascades01:24

Intracellular Signaling Cascades

Once a ligand binds to a receptor, the signal is transmitted through the membrane and into the cytoplasm. The continuation of a signal in this manner is called signal transduction. Signal transduction only occurs with cell-surface receptors, which cannot interact with most components of the cell, such as DNA. Only internal receptors can interact directly with DNA in the nucleus to initiate protein synthesis. When a ligand binds to its receptor, conformational changes occur that affect the...

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Related Experiment Video

Updated: May 16, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

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

Published on: October 19, 2021

Large-scale signaling network reconstruction.

Seyedsasan Hashemikhabir1, Eyup Serdar Ayaz, Yusuf Kavurucu

  • 1Department of Computer Engineering, Middle East Technical University, Ankara 06800, Turkey.

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|December 11, 2012
PubMed
Summary
This summary is machine-generated.

Reconstructing gene signaling networks is challenging. This study integrates RNA interference (RNAi) data with physical interaction networks, developing scalable methods for accurate network topology reconstruction.

Related Experiment Videos

Last Updated: May 16, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

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

Published on: October 19, 2021

Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Reconstructing gene signaling network topology is an underdetermined problem, especially with limited RNA interference (RNAi) data.
  • Existing methods struggle with scalability, being limited to small networks (10-15 genes) due to exponential search spaces.

Purpose of the Study:

  • To develop a scalable computational method for reconstructing signaling network topology.
  • To integrate RNA interference (RNAi) experimental data with prior knowledge from reference physical interaction networks.

Main Methods:

  • Formulated network reconstruction as finding minimum edit operations on a reference network to satisfy RNAi observations.
  • Developed two novel algorithms designed for scalability to large biological networks.

Main Results:

  • The proposed methods provide near-optimal solutions for signaling network reconstruction.
  • Validated on synthetic and real biological data, demonstrating superior scalability compared to existing approaches.
  • The methodology successfully reconstructs networks with up to hundreds of components.

Conclusions:

  • Integrating RNAi data with reference networks offers a robust approach to signaling network topology reconstruction.
  • The developed algorithms significantly improve scalability, enabling analysis of larger and more complex biological systems.
  • The methods generate biologically meaningful results, advancing systems biology research.