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Updated: Jun 19, 2026
07:57
Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
Published on: August 21, 2019
Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions
Holger Fröhlich1, Ozgür Sahin, Dorit Arlt
1German Cancer Research Center, Molecular Genome Analysis, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. h.froehlich@gmx.de
BMC Bioinformatics
|October 10, 2009
Summary
Deterministic Effects Propagation Networks (DEPNs) reconstruct protein signaling networks using gene perturbation and expression data. This robust method aids in understanding complex biological systems and disease mechanisms.
Area of Science:
- Systems Biology
- Molecular Biology
- Bioinformatics
Background:
- Gene perturbation techniques like RNA interference (RNAi) are crucial for studying cellular interventions.
- Integrating perturbation data with expression data provides insights into complex biological systems.
Purpose of the Study:
- To introduce Deterministic Effects Propagation Networks (DEPNs), a novel Bayesian Network approach.
- To enable the reconstruction of protein signaling networks from perturbation and expression data.
Main Methods:
- DEPNs utilize Bayesian Networks to model protein interactions.
- The method incorporates latent network nodes and missing data imputation.
- Robustness was validated using simulated data.
Main Results:
- DEPNs successfully reconstructed the ERBB signaling network in breast cancer cells.
- Protein expression was monitored using Reverse Phase Protein Arrays (RPPAs) after RNAi-mediated protein knockdown.
- The approach was applied to de novo trastuzumab resistant human breast cancer cells.
Conclusions:
- DEPNs provide a robust, efficient, and simple method for inferring protein signaling networks.
- The DEPN methodology and associated data are available in the R package "nem".
- This approach facilitates the analysis of biological networks through multiple interventions.
Related Concept Videos
02:26Protein 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,...
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,...
02:26Protein 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,...
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,...
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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...
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Some...
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