Adjacent gene pairs in the yeast genome have a tendency to
express concurrently. Sharing of regulatory elements within  the 
intergenic region of those adjacent gene pairs was often considered 
the major mechanism responsible for such co-expression. However, 
it is still in debate to what extent that common transcription
factors (TFs) contribute to the co-expression of adjacent genes. 
In order to resolve the evolutionary aspect of this issue, we 
investigated the conservation of adjacent pairs in five yeast
species. By using the information for TF binding sites in promoter 
regions available from the MYBS database 
http://cg1.iis.sinica.edu.tw/~mybs/, the ratios of TF-sharing 
pairs among all the adjacent pairs in yeast genomes were analyzed.
The levels of co-expression in different adjacent patterns were 
also compared.  
Our analyses showed that the proportion of adjacent pairs 
conserved in five yeast species is relatively low compared to that 
in the mammalian lineage. The proportion was also low for adjacent
gene pairs with shared TFs. Particularly, the statistical analysis 
suggested that co-expression of adjacent gene pairs was not
noticeably associated with the sharing of TFs in these pairs. We 
further proposed a case of the PAC (polymerase A and C) and RRPE 
(rRNA processing element) motifs which co-regulate 
divergent/bidirectional pairs, and found that the shared TFs were 
not significantly relevant to co-expression of divergent promoters 
among adjacent genes. 
    Our findings suggested that the commonly shared cis-regulatory
system does not solely contribute to the co-expression of adjacent 
gene pairs in yeast genome. Therefore we believe that during 
evolution yeasts have developed a sophisticated regulatory system 
that integrates both TF-based and non-TF based mechanisms(s) for
concurrent regulation of neighboring genes in response to various 
environmental changes.