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era7 bioinformatics R&D group

Using Gephi with gene ontology graphs

It’s already been a couple of weeks since we started integrating Gephi in some of our services and projects and I must say I’m quite impressed with the results so far.

One of the first uses we found for it was representing gene ontology protein annotations and Go Slim analysis.

Here you can see a graph representation of a protein set gene ontology annotations. Different colors have been applied to each ontology (molecular function, biological process and cellular component). Besides, nodes size is proportional to protein annotations number.

Click here to open the svg in a new window.