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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,...
IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and produces two-second...
Overview of Cell-Matrix Interactions01:24

Overview of Cell-Matrix Interactions

The extracellular matrix or ECM holds cells together to form a tissue and allows the cells within the tissue to communicate. ECM comprises proteins such as fibronectin, collagen, laminin, etc. The most abundant protein in this space is collagen. Collagen fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. ECM allows cell migration and provides a structural scaffold at cell adhesion that anchors the cell when the extracellular matrix proteins interact with...
Overview of Cell Signaling01:23

Overview of Cell Signaling

Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate with the environment.
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...
Overview of Cell Signaling01:23

Overview of Cell Signaling

Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate with the environment.
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...

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Updated: Jul 11, 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

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Inferring cellular networks--a review.

Florian Markowetz1, Rainer Spang

  • 1Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany. florian@genomics.princeton.edu

BMC Bioinformatics
|October 2, 2007
PubMed
Summary

This review overviews computational and statistical methods for reconstructing cellular networks. It organizes current techniques by key concepts like conditional independence models and data from experimental perturbations.

Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Cellular network reconstruction is crucial for understanding biological systems.
  • The field is rapidly evolving with diverse methodologies.
  • A systematic organization of existing methods is needed.

Purpose of the Study:

  • To provide a comprehensive overview of computational and statistical methods for cellular network reconstruction.
  • To organize diverse methods based on fundamental concepts.
  • To highlight approaches for analyzing data from experimental interventions.

Main Methods:

  • Review and synthesis of existing literature on network reconstruction.
  • Categorization of methods based on conditional independence models (e.g., Gaussian graphical models, Bayesian networks).

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  • Discussion of probabilistic and graph-based approaches for perturbation data.

    • Main Results:

    • Most current methods for cellular network reconstruction can be classified under a few core concepts.
    • Conditional independence models offer a framework for network inference.
    • Methods for analyzing perturbation data are essential for understanding network dynamics.

    Conclusions:

    • A conceptual framework aids in understanding the landscape of cellular network reconstruction methods.
    • Integration of different methodological approaches can advance the field.
    • Further development of robust methods is needed for complex biological networks.