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Analysis of Complex Networks by Frank Emmert-Streib, Matthias Dehmer

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11.6 Implications of Pathway Mappings

This section identifies pathways conserved across multiple species, shows how one can resolve enzyme ambiguity, identifies potential holes in pathways, and phylogenetically validates the pathway mappings.

Identifying Conserved Pathways. The authors first identified the pathways that were conserved across all 4 species under consideration. Table 11.2 contains a list of all 20 pathways in B. subtilis that had statistically significant homomorphic images simultaneously in all species. The lower part of Table 11.2 contains 4 more pathways with different names in E. coli, T. thermophilus, and S. cerevisiae, which have simultaneous statistically significant images in all species.

Besides the 24 pathways conserved across all 4 species, this chapter shows that 18 pathways have been found that are only common for triples of these species. Table 11.3 gives the pathway names for each possible triple of species (the triple E. coli, T. thermophilus, and S. cerevisiae does not have extra conserved pathways).

Phylogenetic Validation. One can measure the similarity between species based on the number of conserved pathways. The largest amount of conserved pathways is found between B. subtilis and T. thermophilus –two species-to-species mappings have in total 183 statistically significant pairs of pathways. The next closest two species are E. coli and B. subtilis, which have 126 statistically significant pairs of pathways. This agrees with the fact that B. subtilis ...

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