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 R2 0.0093 0.0100 0.0064 0.0121
p *** *** ** ***
ACMS PPI R2 ns 0.0081 ns 0.0114
p - ** - ***
TATA Box (+/−) R2 0.075551 0.0779 0.06022 0.0752
p *** *** *** ***
Self Interaction (+/−) R2 0.0067 0.0033 0.0038 0.0045
p ** * * *
Gene Essentiality (+/−) R2 0.017441 0.0169 0.01611 0.0211
p *** *** *** ***
Plasticity R2 - - 0.04953 0.0781
p - - *** ***
TATA × Essentiality R2 0.0098 - 0.0060 -
p *** - ** -
Plasticity if TATA(+) R2 - - 0.0279 0.0815
slope - - 0.0010 0.0015
p - - *** ***
Plasticity if TATA(−) R2 - - 0.0219 0.0281
slope - - 0.0004 0.0005
p - - *** ***
TATA × Plasticity R2 - - 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 (1st 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 R2 due to the much larger number of TATA(−) genes. R2 values are shown for each predicting factor in isolation (2nd and 4th numeric columns), as well as, more importantly, for the reduction in the total coefficient of determination R2 when the factor is removed from the best model (1st and 3rd 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

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