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Table 1 Table associated to Figure 1 representing known genetic oscillators that employ transcriptional regulation alone.

From: Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation

Index Bifurcations analysis Reference of the study and remarks Competition
(A) Hopf bifurcation Analytic: Lewis (2003) [41] citing Glass&Mackey (1988) [5] Experimental: Swinburne et al. (2008) [42] -
(B) Hopf bifurcation Analytic: Widder et al. (2007) [43]. The minimum Hill exponent to make oscillations possible is n = 3. -
(C) - Experimental: Atkinson et al. (2003) [6]: The notation 2 + 2 refers to the fact that the DNA loops operate when 2 DNA-bound dimers form a tetramer. It is still not clear if the design functions with competition or not, and this is the reason for employing the 2 + 2 notation instead of the arrows. Probable
(D) - Numeric: Scott et al. (2006) [44] on the Atkinson oscillator. No
(E) SNIC bifurcation Numeric: Guantes&Poyatos (2006) [18] associate their Design I to the Atkinson experimental context. The oscillators they propose due their oscillations to the time-scale difference between activator and repressor life-time. Otherwise, higher multimers than dimers are needed. Yes
(F) Hopf bifurcation Numeric: Hasty et al. (2002) [45] Experimental: Stricker et a. (2008) [7] No
(G) Hopf bifurcation Numeric: Smolen et al. (1998) [46]. The activator needs to be at least a dimer for the existence of the oscillations. Yes
(H) - Experimental and numeric: Elowitz&Liebler (2000) [4]: n = 2 from Figure (1) above makes reference to the value employed by Elowitz&Leibler in their model. See also the discussion in the Supporting Information from Buchler et al. (2005) [47].  
  Hopf bifurcation Analytic: Mueller et al. (2006) [48]: a general case. -