Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context

Table 2 Matrices and matrix pairs of the global context selected by the CMA program

Matrix_ID(1)	TFs(1)	Cut-off(1)	Matrix_ID(2)	TFs(2)	Cut-off(2)	d_min(bp)	d_max(bp)	κ	φ
V$MAZ_Q6	MAZ	0.89						4	0.020763
V$ER_Q6	ER-α	0.913						4	0.047177
V$HEB_Q6	HTF4	0.969						4	0.078905
V$HNF4_Q6_01*	HNF4α, HNF4α2, HNF4γ	0.976						4	0.210340
V$HEN1_02	HEN1	0.854						4	0.099368
V$CREB_Q2*	CRE-BP2, CREM, ATF-1,2,3,4,6	0.888						4	0.086618
V$HNF4_Q6_01*	HNF4α, HNF4α2, HNF4γ	0.8325	V$EFC_Q6	RFX1 (EF-C)	0.6825	8	100	2	0.043344
V$COUP_01	COUP-TF1, COUP-TF2	0.8005	V$KROX_Q6	Egr-1,2,3,4	0.8315	8	100	2	0.053285
V$PEBP_Q6	PEBP2α/AML1,3; PEBP2β	0.84	V$TEL2_Q6	Tel-2a,b,c	0.878	8	100	2	0.214469
V$ELK1_01	Elk-1	0.785	V$WHN_B	FOXN1	0.948	8	100	2	0.111909
V$CMYB_01	c-Myb, B-Myb	0.86	V$KROX_Q6	Egr-1,2,3,4	0.841	8	100	2	0.100922
V$FOXO1_02*	FOXO1,2,4, FOXJ3	0.8715	V$FXR_Q3	FXRα/RXR	0.8135	8	500	2	0.100184
V$HNF4_Q6_01*	HNF4α, HNF4α2, HNF4γ	0.8065	V$HNF4_01 ^(*)	HNF4α, HNF4α2, HNF4γ	0.8705	8	200	2	0.080381
V$XBP1_01	XBP-1	0.8845	V$FOXO1_02 ^(*)	FOXO1,2,4, FOXJ3	0.8715	8	200	2	0.112402

Matrix_ID(1) and Matrix_ID(2) are the TRANSFAC^® identifiers of the selected single matrix (or the first matrix in a pair and the second matrix in the pair, respectively). The other headings of the table correspond to the parameters of the composite module score (see equation 2 in Materials and methods). The first six lines of the table represent the single matrices selected by the algorithm to represent the global context; the other lines represent the pairs of matrices selected by the CMA program. The corresponding values of the parameters (in the Cut-off, κ and φ columns) are optimized by the CMA algorithm. *Matrices corresponding to TFs whose binding site combinatorial co-occupancy was found in Odom et al. [45] for promoters of liver-expressed genes. Bold text indicates TFs identified by the CMA.

ISSN: 1474-760X