Exploring biological networks – the yeast dataset

In 2003, Shiwei Shun, Lunjiang Ling, Nan Zhang, Guojie Li, and Runsheng Chen published a paper titled Topological structure analysis of the protein-protein interaction network in budding yeast in Nucleic Acids Research. As the title of the paper very well conveys, the study involved an analysis of the different interactions between various proteins that are present in yeast. In this recipe, we will consider this protein-protein interaction network of yeast and study its properties. So, let's dive in.

Getting ready

Download the network dataset from https://gephi.org/datasets/yeast.gexf.zip and unzip it into a folder.

How to do it…

The following steps illustrate how to explore and study the properties of the protein-protein interaction network of yeast.

1. Navigate to the folder where you unzipped the downloaded yeast network. You will find a file named yeast.gexf.
2. Double click on the yeast.gexf file to open it in Gephi. This is...