Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality
Figure 5
The automatic method for extraction of ECOBIMs.
Here we demonstrate the major steps of the method on the HC network. The input to the method is a protein interaction network, GO annotation, and the set of essential nodes, which are shown in red. The method considers subnetworks induced by proteins annotated with the same GO biological process term, one subnetwork at a time, to identify densely connected regions or COBIMs. The COBIMs are shown by a COBIM intersection graph, where nodes correspond to COBIMs (the size of the node is proportional to the number of genes in the corresponding COBIM) and there is an edge between a pair of COBIMs if they have at least two proteins in common. The COBIMs that are enriched in essential proteins are selected as ECOBIMs, shown in green.