Table 1 |
|||||
Multiple regression results predicting noise | |||||
Factor | Subtract Factor from Best Model Predicting Noise | Factor in Isolation | Subtract Factor from Best Model Predicting Noise | Factor in Isolation | |
Plasticity Included in Model | |||||
Y2H PPI | R^{2} | 0.0093 | 0.0100 | 0.0064 | 0.0121 |
p | *** | *** | ** | *** | |
ACMS PPI | R^{2} | ns | 0.0081 | ns | 0.0114 |
p | - | ** | - | *** | |
TATA Box (+/−) | R^{2} | 0.07555^{1} | 0.0779 | 0.0602^{2} | 0.0752 |
p | *** | *** | *** | *** | |
Self Interaction (+/−) | R^{2} | 0.0067 | 0.0033 | 0.0038 | 0.0045 |
p | ** | * | * | * | |
Gene Essentiality (+/−) | R^{2} | 0.01744^{1} | 0.0169 | 0.0161^{1} | 0.0211 |
p | *** | *** | *** | *** | |
Plasticity | R^{2} | - | - | 0.0495^{3} | 0.0781 |
p | - | - | *** | *** | |
TATA × Essentiality | R^{2} | 0.0098 | - | 0.0060 | - |
p | *** | - | ** | - | |
Plasticity if TATA(+) | R^{2} | - | - | 0.0279 | 0.0815 |
slope | - | - | 0.0010 | 0.0015 | |
p | - | - | *** | *** | |
Plasticity if TATA(−) | R^{2} | - | - | 0.0219 | 0.0281 |
slope | - | - | 0.0004 | 0.0005 | |
p | - | - | *** | *** | |
TATA × Plasticity | R^{2} | - | - | 0.0075 | - |
p | - | - | ** | - |
^{1} also removed TATA × Essentiality.
^{2} also removed TATA × Essentiality, Plasticity if TATA(+), Plasticity if TATA(−), and restored Plasticity.
^{3} removed Plasticity if TATA(+) and Plasticity if TATA(−).
Models without (1^{st} two numeric columns) and with (last two columns) plasticity as a predictor are shown. After extensive model building, we found that high noise is predicted by low stickiness (low Y2H degree), presence of a TATA box, ability to bind itself, non-essentiality, and high plasticity. A statistically significant interaction term between TATA presence and non-essentiality shows that these two factors have synergistic effects. The TATA × plasticity interaction term is also statistically significant (last row). To provide greater insight, we transformed 3 terms (TATA, plasticity and their interaction) into more intuitive forms (TATA, plasticity if TATA(+), plasticity if TATA(−)). The slope coefficient for plasticity if TATA(+) is 2.5 times larger than that for plasticity if TATA(−), but they make similar contributions to R^{2} due to the much larger number of TATA(−) genes. R^{2} values are shown for each predicting factor in isolation (2^{nd} and 4^{th} numeric columns), as well as, more importantly, for the reduction in the total coefficient of determination R^{2} when the factor is removed from the best model (1^{st} and 3^{rd} numeric columns). Sometimes, as indicated in the footnotes, this involved removing multiple terms and reversing the interaction factor transformation to get a biologically interpretable result. “ns” indicates p > 0.05, * p < 0.05, ** p < 0.01, *** p < 0.001.
Brettner and Masel
Brettner and Masel BMC Systems Biology 2012 6:128 doi:10.1186/1752-0509-6-128