From da54cee73ba091c9537a5e506ef9bf44fa2c2159 Mon Sep 17 00:00:00 2001 From: Kristina Hanspers Date: Sun, 27 Oct 2024 19:57:15 -0700 Subject: [PATCH] Update index.html --- protocols/rna-seq-data-analysis/index.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/protocols/rna-seq-data-analysis/index.html b/protocols/rna-seq-data-analysis/index.html index 65c97be3..cb449ada 100644 --- a/protocols/rna-seq-data-analysis/index.html +++ b/protocols/rna-seq-data-analysis/index.html @@ -86,9 +86,9 @@

Retrieve Networks from STRING

  • Open the example data file, rna-seq-data-cytoscape.csv, in a spreadsheet app and select all gene names, from the Gene Names column. This represents all significantly up- and down-regulated genes.
  • Launch Cytoscape. In the Network Search bar at the top of the Network Panel, select STRING protein query from the drop-down, and paste in the list of genes.
  • Open the options panel and confirm you are searching Homo sapiens with a Confidence cutoff of 0.40 and 0 Maximum additional interactors.
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  • Click the search icon to search. If any of the search terms are ambiguous, a Resolve Ambiguous Terms dialog will appear. Click Import to continue with the import using the default choices. The resulting network will load automatically, and should have around 173 nodes.
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  • Click the search icon to search. If any of the search terms are ambiguous, a Resolve Ambiguous Terms dialog will appear. Click Import to continue with the import using the default choices. The resulting network will load automatically, and should have around 150 nodes.


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