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CoNekT/docs/tutorials/005_coexpression_networks_clusters.md
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# Tutorial: Coexpression Networks and Clusters | |
## Coexpression intro | |
Genes which display a similar expression profile across many samples are considered co-expressed. As co-expression is | |
often attributed to a shared regulatory mechanism, co-expressed genes are likely to be involved in the same biological | |
process. | |
![Coexpression example](images/coexpression_example.png "Coexpression Example") | |
In the example two profiles of co-expressed genes are show, the strength of their co-expression is indicated by the | |
[Pearson Correlation Coefficient](https://en.wikipedia.org/wiki/Pearson_correlation_coefficient) (PCC) which is | |
determined taking all samples into account (not just the ones included inthe profile) | |
## Navigating Coexpression Neighborhoods | |
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") | |
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 | |
visualized using [Cytoscape.js](http://js.cytoscape.org/) of the gene and its coexpression neighborhood. | |
![Coexpression viewer](images/coexpression_viewer.png "Viewer") | |
You are able to pan (by dragging) and zoom (by scrolling) the graph. Node can be selected and moved by dragging. | |
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 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. | |