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CoNekT/docs/tutorials/005_coexpression_networks_clusters.md

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Tutorial: Coexpression Networks and Clusters Coexpression intro Navigating Coexpression Neighborhoods Coexpression Clusters
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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

In the example two profiles of co-expressed genes are show, the strength of their co-expression is indicated by the 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

The table icon table icon can be used to access a table with details on all coexpressed genes. The network icon network icon lead to a network graph visualized using Cytoscape.js of the gene and its coexpression neighborhood.

Coexpression 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

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), network (network icon), profile comparison (profile icon) and heatmap (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

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.