Basic STRING tutorial: Protein query, network views, query parameters, and enrichment visualization
A basic bioinformatics tutorial on how to use the STRING database via its web interface. I first show how to query STRING for a single protein, the difference between the evidence and confidence views, and the effect of various query parameters, namely the confidence cutoff, the maximum number of interactors, and the network type. I continue with very briefly showing the gene set enrichment analysis (GSEA) functionality of STRING, how selected terms can be visualized on the network, and finally how network images can be exported. I recommend that you watch my brief introduction to the STRING database ( • The STRING database: Brief introduction to... ) before watching this tutorial.
0:00 Introduction: the STRING database and overview of the tutorial
0:55 Basic query: single protein query, selecting organism, query disambiguation, and network view
1:54 Settings: evidence view vs. confidence view, changing confidence cutoff, changing maximum number of interactors, and changing from functional associations to physical interactions
4:11 Visualization: enrichment analysis, highlighting of selected terms, and export of network image
Hands-on exercises on STRING are available at https://jensenlab.org/training/string/
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