From 2df8361b71fa14dff4a368786e2f39bab1260353 Mon Sep 17 00:00:00 2001 From: oshorawal <43241051+oshorawal@users.noreply.github.com> Date: Mon, 11 Nov 2024 12:05:26 -0500 Subject: [PATCH] Update visualization.md --- docs/tutorials/visualization.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorials/visualization.md b/docs/tutorials/visualization.md index 6e2b336..5ee03c5 100644 --- a/docs/tutorials/visualization.md +++ b/docs/tutorials/visualization.md @@ -7,7 +7,7 @@ nav_order: 2 # Network Input & Visualization -In this tutorial, we will explore how to customize and visualize a KSI network using PhosNetVis. A kinase substrate enrichment analysis, including but not limited to our fKSEA page, allows you to infer kinases upstream of the observed phosphorylation patterns in a given dataset. Once this kinase substrate enrichment analysis is complete, you can visualize it directly in PhosNetVis. Alternatively, if you have generated the KSI network using another enrichment tool, or would like to customize your KSI network further, this is very easy and convenient to do in the network visualization input file! Just make sure that your input file adheres to the format below for node and edge attributes you would like to customize. In fact, the PhosNetVis network visualization page is fully flexible, and adaptable to any biomolecular network. You can visualize any two connected nodes, not only kinases and substrates, provided that you lable the source and target columns as "Kinase ID" and "Target ID" (e.g. protein, genes, metabolites, etc). This functionality makes the network visualization page adaptable to diverse datasets beyond phosphorylation. You can then upload your network files to PhosNetVis for 2D or 3D visualization. PhosNetVis provides interactive features for exploring the network, such as rotating, zooming, panning, and viewing node information. By the end of this tutorial, you will be able to customize results from any kinase substrate enrichment analysis tool for better visual exploration and analysis in PhosNetVis. **Let’s get started!** +In this tutorial, we will explore how to customize and visualize a KSI network using PhosNetVis. Once you have a KSI network from fKSEA page, you can visualize it directly in PhosNetVis. Or, if you have generated the KSI network using another enrichment tool, or would like to customize your KSI network further, this is very easy to do in the Upload Data for Visualization page! Just make sure that your input file adheres to the formatting guidelines for node and edge attributes you would like to customize. Note that PhosNetVis network visualizations are fully flexible, and adaptable to any biomolecular network! You can visualize any two nodes connected by a directed edge, not only kinases and substrates, provided that you label the source and target columns as “Kinase ID” and “Target ID” (e.g. protein, genes, metabolites, etc). This functionality makes our network visualizations adaptable to diverse datasets beyond phosphorylation. You can then visually explore your networks in 2D or 3D, with or without labels. PhosNetVis provides interactive features for visually exploring the network, such as rotating, zooming, panning, and viewing node information. By the end of this tutorial, you will be able to customize any KSI (or other directed) network for better visual exploration and analysis in PhosNetVis. **Let’s get started!** ***