Month: April 2022

This week I decided to work on a random duplication network. I start with a graph of a ppi network 1 – 20 vertices. I then pick at random a vertex to duplicate. In my case the random choice was 12. I then join this vertex to 11 and 13. I add these new edges to the original network. I do this many times. After doing this 160 times this is the result.

This week I have decided to focus on a scale free networks. I load the ppi network that professor Davis has provided in the class notes into Mathematica. To figure out if a ppi network is scale free you have to construct a table of p(k) versus k. You then have to plot the log of P(k) and the log of k. If the plot shows a straight line then it is a scale free network.
This is a table of P(k) versus k. Lets see a graph of log(P(k)) and log(k).

From this plot we can see there is no straight line meaning this is not a scale free network.

This week I decided to replicate what we learned in the PPI network lecture. I first loaded the protein to protein data into Mathematica, (after great difficulty unzipping the file). After I imported the data I made a graph.

This is a graph of all the connections between the various proteins. We can see that there appears to be some clusters. One big cluster and several smaller clusters. We should plot the bigger cluster separately on another graph.

Here is a 3d version of the same graph.

Next week I would like to do something similar but with another PPI dataset.