Changes between Version 29 and Version 30 of SOPs/go_annotation

Timestamp:

01/26/21 12:22:09 (4 years ago)

Author:

thiruvil

Comment:

--

SOPs/go_annotation

@@ -65 +65 @@
 [[http://bioconductor.org/packages/release/bioc/html/fgsea.html | fgsea]] is an R-package for fast preranked GSEA. This package allows to quickly and accurately calculate arbitrarily low GSEA P-values for a collection of gene sets. You may want to try fgsea if the Broad GSEA takes too long to run. 
 
-=== BiNGO ===
-[[http://chianti.ucsd.edu/cyto_web/plugins/displayplugininfo.php?name=BiNGO|BiNGO Plugin]] \\
-You need to have [[http://cytoscape.org | Cytoscape]] installed to use BiNGO
-  1.  Start BiNGO via Cytoscape , Plugins->Start BiNGO
+=== Cytoscape: BiNGO and ClueGO===
+You need to have [[http://cytoscape.org | Cytoscape]] installed to use BiNGO or ClueGO
+
+[[http://apps.cytoscape.org/apps/bingo|BiNGO Plugin/App]] and [[https://www.psb.ugent.be/cbd/papers/BiNGO/Home.html | documentation]]\\
+
+  1.  Start BiNGO via Cytoscape, Apps->Start BiNGO
   1. Get genes from cluster/network or paste gene list
   1.  Select the correct options (eg. species)
   1.  Run BiNGO
+
+  ''Results'': Each node is color coded by its significance or p-value.  The size of a node represents the number of genes belonging to that GO term or category.
+
+[[http://apps.cytoscape.org/apps/cluego | ClueGO Plugin/App]] and [[http://www.ici.upmc.fr/cluego/| documentation]] \\
+Note:  A [[http://www.ici.upmc.fr/cluego/cluegoLicense.shtml | (free) license key]] is needed to run this tool.
+
+  1.  Start ClueGO via Cytoscape, Apps->Start ClueGO
+  1.  Paste genes
+  1.  Select the correct options (eg. species, database)
+  1.  Run ClueGO (Note: user can use the slide bar to specify how general or detail the terms to be visualized)
+
+  ''Results'': Each node is color coded by its functionally related group it belongs to, a node that contains more than one color implies genes shared with multiple (related) groups.  The size of a node represents the significance of the enrichment.  Edges represent term-term interactions, a thicker edge represents more genes shared between the terms. 
+
+
+
 
 === GeneGO ===