Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast

Brettner, Leandra M; Masel, Joanna

doi:10.1186/1752-0509-6-128

Table 1 Multiple regression results predicting noise

From: Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast

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 (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 R² due to the much larger number of TATA(−) genes. R² 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 R² 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.

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ISSN: 1752-0509

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