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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

Pawar Shrikant et al., KIFCI, a novel putative prognostic biomarker for ovarian adenocarcinomas: delineating protein interaction networks and signaling circuitries. Journal of Ovarian Research (2014) doi:10.1186/1757-2215-7-53

Gachomo W Emma et al., GIGANTUS1 (GTS1), a member of Transducin/WD40 protein superfamily, controls seed germination, growth and biomass accumulation through ribosome-biogenesis protein interactions in Arabidopsis thaliana Development and cell biology. BMC Plant Biology (2014) doi:10.1186/1471-2229-14-37

Baier Herbert et al., ISAAC - InterSpecies Analysing Application using Containers Sequence analysis (applications). BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-18

Mesiti Marco et al., Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction. GigaScience (2014) doi:10.1186/2047-217X-3-5

Pepe Daniele et al., Investigating perturbed pathway modules from gene expression data via structural equation models Transcriptome analysis. BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-132

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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