Table 2.

Mathematical models for steps in gene expression and the regulation at each step by protein and RNA

	Process
Regulator	Chromatin remodeling and histone modification	Transcription (initiation, elongation and termination)	Post-transcriptional processes (capping, poly-adenylation, splicing, interference and RNA degradation)	Translation (initiation, elongation and termination)	Post-translational modification (ubiquitinylation and protein degradation)
Protein	Kim and O’Shea (2008), Luca Mariani (2010)	Kugel and Goodrich (2000)	Cao and Parker (2001), Singh et al. (2007)	Nayak et al. (2011)	Holzhütter and Kloetzel (2000), Peters et al. (2002), Luciani et al. (2005)
Protein feedback	Sedighi and Sengupta (2008), Narula et al. (2010)	Bernard et al. (2006), Rajala et al. (2010)	Model needed	Bar (2009), De Silvaa et al. (2010)	Lee et al. (2010)
RNA	Model needed	Model needed	Levine et al. (2007)	Model needed	Model needed
RNA feedback	Model needed	Model needed	Aguda et al. (2008)	Model needed	Model needed