Kinases are an important family of enzymes that catalyze the transfer of a phosphate group to proteins or molecules. Above, a kinase similarity network (based on the similarity of known-substrates, defined by the cosine distance) is shown as an adjacency matrix. This network includes 404 kinases and 163,216 'links'. The kinases are shown as rows and columns and the links are shown as cells in the matrix. Kinases are shown with two categories: 1) substrate-type (e.g. tyrosine) and 2) kinase-family.
A similarity matrix allows us to visualize this large network without the formation of a 'hairball' that can be associated with traditional ball-and-stick network visualizations. We can see that kinases in this network largely cluster according to their substrate type, which is to be expected. We can zoom into the similarity matrix to see more detailed structures and reorder the matrix using the buttons on the side to help us find other patterns in the data.