Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms
Fig 7
Host-Pathogen Interactions Alignment (HPIA) algorithm.
The HPIA algorithm is a seed-and extend algorithm that aligns two bipartite graphs, e.g., two different host-pathogen protein interaction networks. A) Given an initial pair of seed nodes (red nodes U1 and u1) from two graphs G1 (left) and G2 (right), the algorithm first aligns seed nodes to each other. Then, it aligns the neighbors of the seed nodes from the first graph (green nodes V1-V6) to the neighbors of the seed nodes in the second graph (green nodes v1-v5) based on the node similarity measure (as defined in Equations 6, 8, and 9). This procedure results in six aligned nodes and five aligned edges. B) The algorithm iteratively selects new seeds and extends around them, e.g., it selects nodes V6 from G1 and v5 from G2 as new seed nodes and, based on the node similarity measure, aligns their unaligned neighbors U2 to u2, creating an additional aligned edge (U2-V6 to u2-v5). C) When the algorithm cannot find any seed nodes of the same type that have unaligned neighbors, it greedily aligns all of the remaining unaligned nodes based on their type and the node similarity measure. Some nodes may remain unaligned if the graphs’ sizes vary, e.g., when there is no match for v6 from G2 in G1. The HPIA algorithm generates a list of aligned nodes and a list of aligned edges inferred from the aligned nodes.