<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Interactions between proteins are essential for intracellular communication. They
form complex networks which have become an important source for functional
analysis of proteins. Combining phylogenies with network analysis, we investigate
the evolutionary history of interaction networks from the bHLH, NR and bZIP
transcription-factor families. The bHLH and NR networks show a hub-like structure
with varying γ values. Mutation and gene duplication play an important role
in adding and removing interactions. We conclude that in several of the protein
families that we have studied, networks have primarily arisen by the development of
heterodimerizing transcription factors, from an ancestral gene which interacts with
any of the newly emerging proteins but also homodimerizes.</p>
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Comp Funct Genomics. 2004 Feb; 5(1):79-84