TABLE 1
FROM:
Understanding NF-
B signaling via mathematical modeling
Raymond Cheong, Alexander Hoffmann & Andre Levchenko
doi:10.1038/msb.2008.30
BACK TO ARTICLETable 1: Comparison of published NF-B models
| Model | Predecessor | Feedback | Major changes from predecessor |
|---|---|---|---|
The original mathematical model of NF- B signaling | |||
| Hoffmann et al (2002) | Carlotti et al (2000) | Inducible I B Constitutive I B , IB |  Responsive to IKK stimulus IB negative feedback loop |
| Direct descendants of the original model | |||
| Covert et al (2005) | Hoffmann et al (2002) | Inducible IB Constitutive I B, IB | LPS stimulus modeled as two additive signals offset in time Transcription and translation rates were re-fit |
| O'Dea et al (2007) | Hoffmann et al (2002) | Inducible IB Constitutive I B, IB | IB degradation rates were updated based on experimental measurements |
| Cheong et al (2006) | Hoffmann et al (2002) | Inducible IB, Constitutive I B, IB | IKK time-course generator was added Transcription, translation, and degradation rates were re-fit Nuclear–cytoplasmic volume ratio was added |
| Kearns et al (2006) | O'Dea et al (2007) | Inducible IB Delayed inducible I B, IB | IB and IB are inducible with a 45 min delay IB degradation rates were altered to fit new data |
| Werner et al (2005) | Kearns et al (2006) | Inducible IB Delayed inducible I B, IB | Cubic transcription rate LPS modeled by using its IKK time course as an input |
| Moss et al (2008) | Identical to the model described in Werner et al (2005) | ||
| O'Dea et al (2008) | Werner et al (2005) | Inducible IB Delayed inducible I B, IB | Some rate parameters were modified to model the effect of UV-induced NF-B activity |
| Mathes et al (2008) | Werner et al (2005) | Inducible IB Delayed inducible I B, IB | Some rate parameters were modified to model the effect of IB mutants on NF-B signaling |
| Basak et al (2007) | Werner et al (2005) | Inducible IB, p100 Delayed inducible I B, IB | Introduction of the IB species p100 LPS or TNF induces IKK2-mediated IB degradation LT induces IKK1-mediated p100 degradation |
| Analysis of the original model by MR White and colleagues | |||
| Nelson et al (2004) | Identical to the model described in Hoffmann et al (2002) | ||
| Ihekwaba et al (2004) | Identical to the model described in Hoffmann et al (2002) | ||
| Ihekwaba et al (2005) | Identical to the model described in Hoffmann et al (2002) | ||
| Ihekwaba et al (2007) | Hoffmann et al (2002) | Inducible IB Constitutive I B, IB | Identical to predecessor except some IKK-related parameters changed to match measurements based on experiments where cells were stimulated with IL-1 |
| NF-B models by M Kimmel and colleagues | |||
| Lipniacki et al (2004) | Hoffmann et al (2002) | Inducible IB Inducible A20 | IB and IB were removed from predecessor and A20 negative feedback loop was added New assumptions about IKK activation and deactivation Nuclear–cytoplasmic volume ratio was added Transcription and translation rates were re-fit |
| Lipniacki et al (2006) | Lipniacki et al (2004) | Inducible IB Inducible A20 | Stochastic translation and transcription Some parameters were re-fit |
| Lipniacki et al (2007) | Lipniacki et al (2006) | Inducible IB Inducible A20 | Introduction of TNF receptor and IKK kinase Stochastic TNF receptor activation and IB/A20 transcription |
| Fujarewicz et al (2007) | Lipniacki et al (2004) | Inducible IB Inducible A20 | Equations identical to predecessor but parameters were re-fit |
| Joo et al (2007) | Identical to the model described in Lipniacki et al (2004) | ||
| Other descendants of the original model | |||
| Sung and Simon (2004) | Hoffmann et al (2002) | Inducible IB | IB and IB are removed from predecessor NF-B induction of IB has an explicit transcriptional time delay Some parameters were re-fit |
| Hayot and Jayaprakash (2006) | Hoffmann et al (2002) | Inducible IB | IB and IB are removed, and IB has linear transcription rate Whole model is stochastic |
| Krishna et al (2006) | Hoffmann et al (2002) | Inducible IB | Reduces predecessor to a three-component system with five dimensionless parameters |
| Park et al (2006) | Hoffmann et al (2002) | Inducible IB Constitutive I B, IB | Explicit TNF receptor to IKK pathway IKK activity was affected by factors X and Y representing effects of HBV infection |
| Other NF-B models | |||
| Cho et al (2003) | None | No inducible factors | Tree-like signaling pathway structure with no feedback loops TNF leads either to apoptosis (FADD) or proliferation (NF-B) |
| Monk (2003) | None | Inducible IB | Proposes NF-B oscillations derive from time delay of IB transcription |
| Janes et al (2005) | None | Partial least-squares regression on a large compendium of cytokine signaling data | |
| Janes et al (2006) | Identical to the model described in Janes et al (2005) | ||
| Piotrowska et al (2006) | None | No inducible factors | Two-component system with five dimensionless parameters Negative correlation between IB and NF-B is directly assumed Proliferation rate is a function of NF-B |
| Pogson et al (2006) | None | No inducible factors | Agent-based stochastic simulation Incorporates events from receptor activation to NF-B nuclear import |
| Rangamani and Sirovich (2007) | None | Inducible IB Inducible IAP | TNF leads either to apoptosis (caspase) or survival (NF-B) IB and IB are not present Parameters were taken from a variety of sources |
