At the moment one type of analysis of transcription regulatory networks (TRNs) in prokaryotes is topological analysis of graph structure of possible regulatory interaction links (see for example [1]). That type of analysis takes into account possibility links that designate the fact that one gene product in some conditions can modulate transcription of the other. The benefit of such approach is that it is allow analyzing TRN at the whole cell level. At the same type it is known that at least some responses are regulated by abundance of elements of transcription machinery [2-3]. We have developed conceptual model of whole cell E. coli TRN with SBGN ER, SBGN PD and SBGN AF languages [4]. That model is the first step towards incorporation of some quantitative information into whole cell TRN modeling.

1.	Freyre-González et al. Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach. Genome Biol (2008) vol. 9 (10) pp. R154
2.	Klumpp and Hwa. Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc Natl Acad Sci USA (2008) vol. 105 (51) pp. 20245-50
3.	Barker et al. Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J Mol Biol (2001) vol. 305 (4) pp. 689-702
4.	Le Novère et al. The systems biology graphical notation. Nature biotechnology (2009) vol. 27 (8) pp. 735-41

