In this article, we will see how to use Cytoscape to visualize biological networks. A network is a set of nodes (such as people) connected by edges (such as friendship). Some examples in biology are:
- gene-gene networks to identify co-expressed genes in a cell
- gene-protein networks to study the regulation of gene expression by transcription factors
- protein-protein networks to characterize signaling pathways in a cell
- metabolite-metabolite networks to study biochemical reactions in an organism
- cell-cell networks to identify interactions between neurons or immune cells
- organism-organism networks to study social interactions within species or predator/prey interactions between species
Data preparation
To visualize biological networks in Cytoscape, we need to prepare an input file listing the pairs of nodes that are connected. Each row corresponds to an interaction between a source node and a target node. Here is an example file for a gene-gene network (gene names are invented):
Data import
To open a file in Cytoscape, we need to click on: File, Import, Network from File. After selecting the file, we need to define which column corresponds to the source node and which column corresponds to the target node. This is done automatically if the columns are already named “source_node” and “target_node” in the file:
Then, Cytoscape directly creates the network(s). As you can see in the image below, my file contains three separate networks:
Plot modification
To change the aesthetics of the plot, we can select one or several network(s) with the CTRL button pressed and the mouse. When selected, the network appears in yellow instead of blue. After that, we need to select the “Style” tab instead of the “Network” tab:
A lot of parameters can be modified for the nodes (height, width, fill color, border color, label color,…), for the edges (line type, arrow shape,…) and for the networks (background color):
Plot export
Finally, to export the network image in JPEG, PNG or other formats, we need to click on: File, Export, Network to Image. Finally, here is the final result after cropping:
Conclusion
In conclusion, the visualization of biological networks is really easy in Cytoscape!
