I would be interested to know if there is a method/analysis or a set of methods to compare two groups of pathways or families of proteins.
I would specifically be interested by a system biology approach which takes all the components of the pathway or family of proteins. I would like to know if there is a method which can not only compare the similarity, homology, divergence and convergence of a family of proteins (like ribosomal proteins) between species but also between groups in the same organism.
For example I would like to compare the molecular components of vesicular trafficking pathways to the molecular components of non-vesicular pathway in the same organism saccharomyces cerevisiae (yeast).
I would greatly appreciate your suggestions.