diff --git a/docs/tutorials/005_coexpression_networks_clusters.md b/docs/tutorials/005_coexpression_networks_clusters.md index d04139b..7c48d54 100644 --- 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 \ No newline at end of file diff --git a/docs/tutorials/images/go_enrichment_entry.png b/docs/tutorials/images/go_enrichment_entry.png new file mode 100644 index 0000000..8543441 Binary files /dev/null and b/docs/tutorials/images/go_enrichment_entry.png differ diff --git a/docs/tutorials/images/heatmap_icon.png b/docs/tutorials/images/heatmap_icon.png new file mode 100644 index 0000000..bdaa258 Binary files /dev/null and b/docs/tutorials/images/heatmap_icon.png differ diff --git a/docs/tutorials/images/profile_icon.png b/docs/tutorials/images/profile_icon.png new file mode 100644 index 0000000..e0ddef3 Binary files /dev/null and b/docs/tutorials/images/profile_icon.png differ