Identify key information in a Sequence Similarity Network and create a publication ready Figure
Channel: Enzyme Function
Date: 10/07/2019

In the Cytoscape "Control panel", the general style of networks can be edited. I show how to change the default styling to create images that are suited as Figures for publications, and how to export such an image.

It is important to identify in SSNs, nodes that have SwissProt descriptions:
In the UniProt database, some sequences have a SwissProt description (or annotation). Those correspond to records with information extracted from literature and curator-evaluated computational analysis. We consider sequences that have SwissProt description as references sequences that can and should be trusted for SSN analysis.

I show how to locate, in a network, the Nodes that have a SwissProt description, using the Select function in the Cytoscape control panel.
In some cases, nodes are not very visible, because embedded within a cluster. I demonstrate how to bring selected nodes on top by using the depth parameter, so they become visible.

In our example SSN, three types of SwissProt descriptions are present. I color each of them individually.

I locate a node of interest, using the general search function, and edit its style
I add relevant Text annotations to the network. 

After manipulating this network, I save my work as a .cys cytoscape session file, so I can reload it, if needed, for later work.

I export a final image that can be used as a Figure for a publication.

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The Enzyme Function Initiative (EFI) website (https://efi.igb.illinois.edu/) contains a collection of webtools for creating and analyzing Sequence Similarity Networks (SSNs) and Genome Neighborhood Networks (GNNs). Created SSNs need to be downloaded. The file format outputted by the EFI website is .xgmml. Cytoscape (https://cytoscape.org/) is a software for visualizing networks and integrating these with any type of attribute data that allows to open, visualize and manipulate SSNs.