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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,...
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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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

Global networks of functional coupling in eukaryotes from comprehensive data integration.

Andrey Alexeyenko1, Erik L L Sonnhammer

  • 1Stockholm Bioinformatics Center, Albanova, Stockholm University, 10691 Stockholm, Sweden.

Genome Research
|February 28, 2009
PubMed
Summary

Computational methods can integrate diverse data to map functional coupling (FC) networks. FunCoup, a Bayesian framework, accurately predicts these networks across species, aiding disease pathway discovery.

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Systems biology

Background:

  • Experimental methods alone cannot fully map the complex interactome.
  • Integrating diverse proteomics and genomics data presents challenges in scale and heterogeneity.
  • Accurate reconstruction of global functional coupling (FC) networks is crucial for understanding biological systems.

Purpose of the Study:

  • To develop an optimized computational framework for reconstructing global functional coupling networks.
  • To address the challenges of scale and data heterogeneity in interactome mapping.
  • To enhance the accuracy and confidence of predicted biological networks.

Main Methods:

  • Developed FunCoup, an optimized Bayesian framework for integrating heterogeneous data.
  • Annotated network edges with confidence scores for various interaction types (physical, complex, metabolic, signaling).
  • Utilized over 50 datasets across seven organisms, transferring information between orthologs.

Main Results:

  • Predicted global functional coupling networks in eight eukaryotes with high accuracy.
  • Demonstrated improved accuracy by annotating interaction types.
  • Validated predictions using independent cancer mutation data and cross-species pathway conservation.
  • Successfully predicted candidate members for Parkinson and Alzheimer disease pathways.

Conclusions:

  • FunCoup provides a robust and scalable computational approach for interactome reconstruction.
  • The framework's ability to integrate diverse data and annotate interaction confidence significantly boosts accuracy.
  • FunCoup predictions offer valuable insights for disease pathway discovery and understanding cross-species biological conservation.