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known and predicted protein-protein interactions

Tutorial and training materials by OpenHelix

Learn to use STRING, a database of known and predicted protein-protein interactions. Predictions are based on a series of evidences such as gene neighborhood, patterns of co-expression, text-mining of the literature and more. STRING allows the user to view data from individual evidences of interaction or view a 'network' of interactions among a collection of proteins. Learn to use this resource and find interaction predictions to facilitate characterization of gene and protein function.
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You'll learn:

  • how to search for predicted interactions with a selected gene product
  • how to view networks of interactions among individual molecules or COGs
  • the many types of evidences of interaction and how to analyze them
  • how to find information from outside sources used in the predictions


Related tutorials

This tutorial is a part of the tutorial group Bork Group Resources. You might find the other tutorials in the group interesting:

  • XplorMed: eXploring Medline abstracts
  • SMART: Protein domain annotation and analysis of domain architectures

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Recent BioMed Central research articles citing this resource

Marshall John et al., Creation of a federated database of blood proteins: a powerful new tool for finding and characterizing biomarkers in serum. Clinical Proteomics (2014) doi:10.1186/1559-0275-11-3

Fengos Georgios et al., Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome Science (2014) doi:10.1186/1477-5956-12-23

Chou Hsiu-Chuan et al., Effect of glutathione reductase knockdown in response to UVB-induced oxidative stress in human lung adenocarcinoma. Proteome Science (2014) doi:10.1186/1477-5956-12-2

Sheydina Anna et al., Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase Structural analysis. BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-112

Sánchez-Rodríguez Aminael et al., A network-based approach to identify substrate classes of bacterial glycosyltransferases Prokaryote microbial genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-349

More about the resource:

The STRING database of predicted molecular interactions was developed by the Bork Lab at the European Molecular Biology Laboratory (EMBL) in Heidelberg Germany. Predictions are based on a series of evidences and given scores of probability. Researchers can search for specific protein interactions (using gene name or other identifiers) or search for COG (Cluster of Orthologous Groups) predicted interactions. Most data views link out to other more detailed databases. This resource is a free publicly available tool.


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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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