Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding

BMC Genomics

Table 1 Modeling c-Jun, GR and Hoxa2 binding using a logistic regression

Evaluated parameters	AP-1 motif			GR motif			Pbx motif
	(TGA^C/_GTCA)(11,926/271,973)			(G-ACA---TGT-C)(1,393/27,176)			(TGATTGAT)(638/59,802)
	PVE(%)	CV err.	AUC	PVE(%)	CV err.	AUC	PVE(%)	CV err.	AUC
A1. Peak	10.3	0.04	0.76	2.9	0.05	0.63	0.5	0.01	0.57
A2. Background	6.5	0.04	0.70	3.0	0.05	0.64	0.1	0.01	0.50
A3. Relative peak	1.9	0.04	0.62	0.2	0.05	0.53	0.6	0.01	0.57
A. INOS (A1+A2+A3)	11.5	0.04	0.77	3.9	0.05	0.66	0.6	0.01	0.57
B. Overlap with CGIs	0.9	0.04	0.53	0.1	0.05	0.51	0.0	0.01	0.51
C. Cluster of canonical motifs	5.5	0.04	0.66	0.6	0.05	0.51	0.1	0.01	0.51
D. Co-occurrence of 2nd motif*	0.2	0.04	0.51	2.6	0.05	0.57	0.1	0.01	0.51
A+B	12.3	0.04	0.78	3.9	0.05	0.66	0.6	0.01	0.57
A+B+C	13.9	0.04	0.79	4.2	0.05	0.67	0.7	0.01	0.58
A+B+C+D	14.0	0.04	0.79	6.7	0.05	0.70	0.8	0.01	0.58

Modeling the c-Jun binding to AP-1 motif (TGA^C/_GTCA), GR binding to GR motif (G-ACA---TGT-C), Hoxa2 binding to Pbx motif (TGATTGAT) were performed by the logistic regression using generalized linear models (GLM). PVE Percent of variance explained (%) = 1-(deviance/null.deviance). CV err. estimated 11-fold cross-validation prediction error, AUC Area under the ROC curve. *The Co-occurrence of 2nd motifs: the co-occurrence motif of AP-1 motif is GR motif (G-ACA---TGT-C), the co-occurrence of GR motif is AP-1 motif (TGA^C/_GTCA), the co-occurrence of Pbx motif is GR-like 8-mer (G-TGA---ATG-C). The PVEs of INOS and Co-occurrence of 2nd motif for AP-1, GR and Pbx motif are shown in bold to highlight the difference between the motifs.

ISSN: 1471-2164