It may be significant that eight of the twelve cases in Table 1 involve only two branches, namely branches 4 and 112.
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Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species.
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The sentences
While there are many factors determining whether a gene is activated or deactivated, it seems likely to be significant if the probability of a transcription factor is high for a branch of the phylogenetic tree and lower for the remaining species, or vice versa.