BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors

Table 1 Condition-specific binding parameters for three yeast TFs.

Binding behavior	TF name	Environment	E _BP	U _BP	Motif similarity score
Condition enabled	MSN2	YPD	-21.96	-13.97	0.76
	MSN2	H ₂ O ₂ hi	-18.43	-17.57	0.92
	MSN2	H ₂ O ₂ lo	-21.54	-16.64	0.91
Condition expanded	GCN4	YPD	-23.84	-22.73	0.94
	GCN4	Sm	-24.26	-21.68	0.93
	GCN4	Rapa	-24.54	-21.27	0.94
Condition altered	STE12	YPD	-17.80	-16.40	0.91
	STE12	But14	-26.45	-22.14	0.92
	STE12	Alpha	-20.71	-19.25	0.89

Minimal binding energy (consensus) E_BPand chemical potential U_BPare estimated by the BayesPI using ChIP-chip experimental data under various conditions [27], such as rich medium condition (YPD), a high hyperoxic (H₂O₂hi), a moderate hyperoxic (H₂O₂lo), amino acid starvation (Sm), nutrient deprived (Rapa), filamentation inducing (But14) and mate inducing (Alpha).

ISSN: 1471-2105