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STRING: a database of predicted functional associations between proteins.

Christian von Mering1, Martijn Huynen, Daniel Jaeggi

  • 1European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Nucleic Acids Research
|January 10, 2003
PubMed
Summary
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The STRING database predicts functional protein associations using genomic data. It offers a scoring framework to assess interaction significance and visualize networks for biological analysis.

Area of Science:

  • Genomics
  • Bioinformatics
  • Systems Biology

Background:

  • Functional protein links can be inferred from genomic associations of encoding genes.
  • Gene groups with similar functions exhibit comparable species distribution and genomic proximity.
  • Gene fusion events also indicate functional relationships between genes.

Purpose of the Study:

  • To present the STRING database as a global resource for exploring and analyzing genomic associations.
  • To introduce a unique scoring framework for assessing the significance of predicted protein interactions.
  • To enable high-level visualization of functional linkage networks and facilitate modularity analysis.

Main Methods:

  • Utilizing genomic associations (species coverage, gene proximity, gene fusions) to infer functional links.

Related Experiment Videos

  • Developing a scoring framework based on benchmarks against a reference set for confidence scoring.
  • Implementing graphical network representation for visualizing inferred protein interactions.

    • Main Results:

    • STRING database contains 261,033 orthologs across 89 genomes.
    • A confidence score is integrated for each predicted interaction.
    • Functional interactions are predicted with at least 80% accuracy for over half of the genes.

    Conclusions:

    • STRING provides a valuable resource for understanding functional protein associations.
    • The scoring framework allows for robust assessment of interaction significance.
    • Network visualization aids in analyzing biological modularity and functional linkage.