Table 3. Effects of cooperative DNA binding by the primary TF and a secondary TF (“M2”), that were significant at distance threshold either 30 bp or 150 bp.

Data set	M2	CC(M1)	CC(M1+M2); 30 bp	ImprOverM1; 30 bp	CC(M1+M2); 150 bp	ImprOverM1; 150 bp	Tag
BIN_Fchip_s10_11	ADF1	0.630	-	-	0.676	0.047	*
BIN_Fchip_s10_11	BRK	0.630	-	-	0.682	0.052
BIN_Fchip_s10_11	MAD	0.630	-	-	0.686	0.056
CAD_Bseq_s5	ADF1	0.178	-	-	0.391	0.212
CAD_Bseq_s5	CG7928	0.178	0.254	0.076	0.257	0.079
CAD_Bseq_s5	DL	0.178	0.268	0.089	0.268	0.090
CAD_Bseq_s5	TTK	0.178	0.286	0.107	0.328	0.150
D_Mseq_s5_11	ADF1	0.328	0.380	0.052	-	-	*
D_Mseq_s5_11	HLHM5	0.328	-	-	0.416	0.088	*
D_Mseq_s5_11	MAD	0.328	0.380	0.052	-	-	*
D_Mseq_s5_11	TTK	0.328	-	-	0.400	0.072	*
D_Mseq_s5_11	ESPL	0.328	0.373	0.045	0.415	0.087
D_Mseq_s5_11	HLHMBETA	0.328	0.378	0.050	0.394	0.066
EN_Mchip_s5_14	TTK	0.321	0.388	0.067	0.391	0.070	*
EVE_Mseq_s14	ARA	0.174	0.291	0.116	0.268	0.094
EVE_Mseq_s14	CAUP	0.174	0.291	0.116	0.275	0.100
GT_Bseq_s5	TTK	0.241	-	-	0.288	0.047
HB_Bchip_s9	ADF1	0.204	0.303	0.099	-	-	*
HB_Bchip_s9	WOR	0.204	0.312	0.107	0.308	0.103
HB_Bseq_s5	ADF1	0.374	0.427	0.053	-	-
MED_Bchip_s10	PNR	0.184	-	-	0.226	0.042
MED_Bchip_s10	SIX4	0.184	0.224	0.040	0.227	0.043
MED_Bchip_s14	ZIF	0.255	-	-	0.337	0.082	*
MED_Bchip_s14	RIB	0.255	0.341	0.086	-	-	*
MED_Bchip_s14	TTK	0.255	-	-	0.331	0.075	*
MED_Bchip_s5	DEAF1	0.102	0.153	0.051	-	-	*
MED_Bchip_s5	HB	0.102	0.165	0.063	-	-	*
RUN_Bchip_s5	TTK	0.258	-	-	0.304	0.046
SLP1_Bchip_s5	ADF1	0.214	0.263	0.049	0.290	0.076
SLP1_Bchip_s5	TTK-PF	0.214	-	-	0.275	0.061
TIN_Fchip_s10_11	Z	0.392	-	-	0.438	0.046
TLL_Bchip_s5	DL	0.159	-	-	0.206	0.047
TWI_Bchip_s5	DL	0.251	-	-	0.319	0.068
TWI_Fchip_s10_11	Z	0.405	-	-	0.445	0.040
TWI_Fchip_s9	TIN	0.420	-	-	0.465	0.045

Only cases involving secondary motifs other than “VFL” and “TRL”, and where P-value≤0.05 and Z-score ≥3 are shown here. Cases where the improvement at distance threshold 30 bp was similar to or better than that at 150 bp are highlighted in bold. Dashes indicate that the secondary motif was not observed to show significant improvement at the specific distance threshold. This table presents results from testing all secondary motifs whose TFs were in the top 25% most highly expressed TF genes (out of the ∼300 TF genes with motifs) in the appropriate developmental stage. This is contrast to other tables (2, 3, 4, 6), where the tested secondary motifs correspond to TFs that are in the top 10–15% most highly expressed TF genes for the stage. In this table, the rows marked with asterisks correspond to secondary TFs in the top 10–15% most highly expressed TF genes.