tutorial/manual

proost · Dec 5, 2017 · c118fc6 · c118fc6
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diff --git a/docs/tutorials/005_coexpression_networks_clusters.md b/docs/tutorials/005_coexpression_networks_clusters.md
@@ -17,7 +17,7 @@ determined taking all samples into account (not just the ones included inthe pro
 
 A gene's coexpressed genes (referred to as the coexpression neighborhood) can be found on the sequence page.  
 
-![Coexpression entry(images/coexpression_entry.png "Coexpression Entry")
+![Coexpression entry](images/coexpression_entry.png "Coexpression Entry")
 
 The table icon ![table icon](images/table_icon.png "table icon") can be used to access a table with details on all 
 coexpressed genes. The network icon ![network icon](images/network_icon.png "network icon") lead to a network graph
@@ -30,11 +30,33 @@ Furthermore on the top-right corner there is a control bar.
 
 ![Control bar](images/control_bar.png "Control bar")
 
-From left to right, there is the "Reset View button" which will zoom the graph to fit the window. The search box where
-a gene ID, IntePro domain or GO term can be entered to highlight all matching genes, then there is the Node, edge and 
-layout controls which can be used to change the appearance of the nodes, edges and layout repectively. The right-most
-button is the export button which allow you to export the graph as an image (PNG and SVG are supported) or to a format
+From left to right, there is the **Reset View** button which will zoom the graph to fit the window. The **search box** 
+where a gene ID, IntePro domain or GO term can be entered to highlight all matching genes, then there is the **node**, **edge** 
+and **layout** controls which can be used to change the appearance of the nodes, edges and layout respectively. The right-most
+button is the **export** button which allow you to export the graph as an image (PNG and SVG are supported) or to a format
 which can be loaded in third party (XGMML) tools for local analysis.
 
+## Coexpression Clusters 
+
+The coexpression network can also be compartmentalized using algorithms into more manageable clusters. These can be
+accessed from the sequences directly as a table (![table icon](images/table_icon.png "table icon")), 
+network (![network icon](images/network_icon.png "network icon")), 
+profile comparison (![profile icon](images/profile_icon.png "profile icon")) and 
+heatmap (![heatmap icon](images/heatmap_icon.png "heatmap icon")).
+
+In CoNekT functional enrichment for clusters is pre-calculated and enrichment for phylostrata/clades. The former can 
+shed light on the function of the cluster's members including those which currently lack annotation. The latter hints
+at the point in time when this feature evolved. To pick up co-expression clusters of interest, a search function is 
+provided in the tools menu, under **Find enriched clusters**.
+
+![GO enrichment entry](images/go_enrichment_entry.png "GO enrichment")
+
+After specifying parameters, the **Count** button can be clicked to find out how many clusters meet the current criteria.
+
+When looking for clusters enriched for **plant-type cell wall biogenesis** in *Arabidopsis thaliana*, leaving other options
+at their default values eight clusters are found. This included **Cluster_66** which contains CESA1 , CESA6 one of the cellulose 
+synthases and **Cluster_148** which contains Cellulose Synthase like proteins. The other genes, lacking functional 
+annotation, in these clusters would be good canditates to knock out and test the phenotype of mutants for defects in their
+roots.
+
 
-## Coexpression Clusters 
diff --git a/docs/tutorials/images/go_enrichment_entry.png b/docs/tutorials/images/go_enrichment_entry.png
diff --git a/docs/tutorials/images/heatmap_icon.png b/docs/tutorials/images/heatmap_icon.png
diff --git a/docs/tutorials/images/profile_icon.png b/docs/tutorials/images/profile_icon.png