We implement a strategy for aligning two protein-protein interaction networks that combines interaction topology and protein sequence similarity to identify conserved interaction pathways and complexes. Using this approach we show that the protein-protein interaction networks of two distantly related species, Saccharomyces cerevisiae and Helicobacter pylori… (More)
Fig. 1. Example pathway alignment and merged representation. (a) Vertical solid lines indicate direct protein–protein interactions within a single pathway, and horizontal dotted lines link proteins with significant sequence similarity (BLAST E value Ecutoff). An interaction in one pathway may skip over a protein in the other (protein C), introducing a ‘‘gap.’’ Proteins at a particular position that are dissimilar in sequence (E value Ecutoff, proteins E and g) introduce a ‘‘mismatch.’’ The same protein pair may not occur more than once per pathway, and neither gaps nor mismatches may occur consecutively. (b) Pathways are combined as a global alignment graph in which each node represents a homologous protein pair and links represent protein interaction relationships of three types: direct interaction, gap (one interaction is indirect), and mismatch (both interactions are indirect).