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Although it is well known that genes, proteins, and pathways are conserved across evolution, conservation of interactions between genetic pathways having the potential to differentially regulate expression of phenotypes is only just beginning to be characterized in model systems [ 61, 62].
We propose explanatory mechanisms based on indirect effects and discuss the implications of our results for the conservation of interactions and communities.
Comparison of lamprey ER and human ERα in Figures 4 and 5 reveals a conservation of interactions of the A ring of E2 and 15α-OH-E2 with lamprey ER and human ER.
The above discussion illustrates several (sometimes conflicting) trends observed for the conservation of interactions across species.
The link-based baseline takes only direct interaction partners into account, again independently of conservation of interactions.
We anticipated the presence of false positives in predicted interactions due to the lack of evolutionary conservation of interactions.
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We are exploring this property of conservation of interaction as a means to assign protein functions by concentrating on protein-protein interaction (PPI) pairs with similar interacting modular domain patterns.
Recent high throughput experiments with better coverage [ 13, 14] made it possible to reassess the conservation of interaction data.
While the results in these early papers indicated low overlap between species, no attempt was made to generalize observations to address reasons for the lower conservation of interaction data when compared to sequence data conservation.
Another recent study by [ 10] has also measured the coherency of evolutionary conservation of interaction patterns in an integrated network of S. cerevisiae comprising transcriptional and protein-protein interaction data.
The utility and evolutionary conservation of interaction networks in these and other genetically tractable metazoan organisms is well established, making them powerful models for exploring human biology and disease mechanisms [ 52- 55].
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