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khanspers authored Oct 28, 2024
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Expand Up @@ -86,9 +86,9 @@ <h1>Retrieve Networks from STRING</h1>
<li>Open the example data file, <b>rna-seq-data-cytoscape.csv</b>, in a spreadsheet app and select all gene names, from the <b>Gene Names</b> column. This represents all significantly up- and down-regulated genes.</li>
<li>Launch Cytoscape. In the <highlight>Network Search</highlight> bar at the top of the <highlight>Network Panel</highlight>, select <highlight>STRING protein query</highlight> from the drop-down, and paste in the list of genes.</li>
<li>Open the options panel <img class="plain" src="string-options.png" style="height:30px"> and confirm you are searching <b>Homo sapiens</b> with a <b>Confidence cutoff</b> of <b>0.40</b> and <b>0 Maximum additional interactors</b>.</li>
<li>Click the search icon <img class="plain" src="SearchIcon.png" style="height:30px"> to search. If any of the search terms are ambiguous, a <highlight>Resolve Ambiguous Terms</highlight> dialog will appear. Click <highlight>Import</highlight> to continue with the import using the default choices. The resulting network will load automatically, and should have around 173 nodes.</li>
<li>Click the search icon <img class="plain" src="SearchIcon.png" style="height:30px"> to search. If any of the search terms are ambiguous, a <highlight>Resolve Ambiguous Terms</highlight> dialog will appear. Click <highlight>Import</highlight> to continue with the import using the default choices. The resulting network will load automatically, and should have around 150 nodes.</li>
</ul> <br /><br />
<img class="plain" src="string-search.png">
<img class="plain" src="string-search.png" style="height:450px">
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<img class="plain" src="string-search.png" />
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