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)
 dmin (bp)
 dmax (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.

Kel et al. Genome Biology 2008 9:R36   doi:10.1186/gb-2008-9-2-r36