Abstract
BackgroundThe regulatory interactions between transcription factors (TF) and regulated genes (RG) in a species genome can be lumped together in a single directed graph. The TF's and RG's conform the nodes of this graph, while links are drawn whenever a transcription factor regulates a gene's expression. Projections onto TF nodes can be constructed by linking every two nodes regulating a common gene. Similarly, projections onto RG nodes can be made by linking every two regulated genes sharing at least one common regulator. Recent studies of the connectivity pattern in the transcription-factor regulatory network of many organisms have revealed some interesting properties. However, the differences between TF and RG nodes have not been widely explored.ResultsAfter analysing the RG and TF projections of the transcription-factor gene regulatory networks of Escherichia coli and Saccharomyces cerevisiae, we found several common characteristic as well as some noticeable differences. To better understand these differences, we compared the properties of the E. coli and S. cerevisiae RG- and TF-projected networks with those of the corresponding projections built from randomized versions of the original bipartite networks. These last results indicate that the observed differences are mostly due to the very different ratios of TF to RG counts of the E. coli and S. cerevisiae bipartite networks, rather than to their having different connectivity patterns.ConclusionSince E. coli is a prokaryotic organism while S. cerevisiae is eukaryotic, there are important differences between them concerning processing of mRNA before translation, DNA packing, amount of junk DNA, and gene regulation. From the results in this paper we conclude that the most important effect such differences have had on the development of the corresponding transcription-factor gene regulatory networks is their very different ratios of TF to RG numbers. This ratio is more than three times larger in S. cerevisiae than in E. coli. Our calculations reveal that, both species' gene regulatory networks have very similar connectivity patterns, despite their very different TF to RG ratios. An this, to our consideration, indicates that the structure of both networks is optimal from an evolutionary viewpoint.
Highlights
The regulatory interactions between transcription factors (TF) and regulated genes (RG) in a species genome can be lumped together in a single directed graph
Since E. coli is a prokaryotic organism while S. cerevisiae is eukaryotic, we investigate in this work the possibility that the above referred differences emerge at the whole network level and can be identified via network theory analysis
Global and projected network topology The E. coli and S. cerevisiae gene regulatory networks are bipartite; i.e. they comprise two kinds of nodes, transcription factors (TF) and regulated genes (RG), with the links being directed from the TF to the RG nodes
Summary
The regulatory interactions between transcription factors (TF) and regulated genes (RG) in a species genome can be lumped together in a single directed graph. Recent studies of the connectivity pattern in the transcription-factor regulatory network of many organisms have revealed some interesting properties. We know the genome-wide transcription-factor regulatory networks of various species. The advantages of network theory are that: it allows the description of a network structure with graph concepts, and reveals organizational features shared with numerous other biological and nonbiological networks; it is possible with network theory to quantitatively describe networks of hundreds or thousands of interacting components; and in some cases, the observed network topology gives clues about its evolution, and the observed network organization may help to elucidate its function and dynamic responses [17]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
