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# Tutorial: Coexpression Networks and Clusters

## Navigating Coexpression Networks
## 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 Clusters
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