The orientation of transcription factor binding site motifs in gene promoter regions: does it matter?

Lis, Monika; Walther, Dirk

doi:10.1186/s12864-016-2549-x

BMC Genomics

Table 5 Motif pairs with pronounced non-random motif order and orientation preferences

From: The orientation of transcription factor binding site motifs in gene promoter regions: does it matter?

Motif 1	Motif 2	Motif 1 - Motif 2				Motif 2 -Motif 1				p_BH Entropy	p_BH Expr	Cohen’s d
Motif 1	Motif 2	++	+−	--	−+	++	+−	--	−+	p_BH Entropy	p_BH Expr	Cohen’s d
Bellringer/replumless/pennywise_BS1_IN_AG	Bellringer/replumless/pennywise_BS1_IN_AG	405	283	322	316	405	283	322	316	0.00E + 00	6.99E-01	1.82E-02
TELO-box_promoter motif	TELO-box_promoter motif	200	35	165	10	200	35	165	10	0.00E + 00	2.96E-02	−1.96E-01
M2217_1.01	M2217_1.01	129	29	125	16	129	29	125	16	0.00E + 00	6.99E-01	−6.87E-02
M0769_1.01	M0769_1.01	43	10	20	17	43	10	20	17	0.00E + 00	6.09E-01	−1.52E-01
MYB1_binding_site motif	MYB1_binding_site motif	61	4	10	2	61	4	10	2	0.00E + 00	NA	NA
Gap-box_motif	Gap-box_motif	22	14	29	6	22	14	29	6	0.00E + 00	6.99E-01	−1.28E-01
Gap-box_motif	TELO-box_promoter motif	30	10	43	11	8	12	18	5	0.00E + 00	6.99E-01	2.59E-01
SBOXATRBCS	M0769_1.01	0	5	1	21	21	3	0	3	0.00E + 00	9.05E-01	1.25E-01
MYB1_binding_site motif	TELO-box_promoter motif	19	8	13	4	11	2	6	4	1.40E-03	6.99E-01	−2.65E-01
TELO-box_promoter motif	M0769_1.01	21	13	17	16	26	19	38	8	1.40E-03	7.65E-01	−5.71E-02
TELO-box_promoter motif	M1561_1.01	2	8	11	16	9	1	8	14	1.40E-03	6.99E-01	−3.64E-01
MYB3_binding_site motif	MYB3_binding_site motif	15	2	5	6	15	2	5	6	1.55E-03	8.56E-02	−1.02E + 00
Bellringer/replumless/pennywise_BS1_IN_AG	M2251_1.01	35	25	22	23	28	9	13	14	2.02E-03	6.99E-01	−9.38E-02
M0758_1.01	M0758_1.01	415	330	408	404	415	330	408	404	3.77E-03	1.45E-01	−9.02E-03
Bellringer/replumless/pennywise_BS1_IN_AG	M0758_1.01	274	318	313	287	341	245	272	322	4.65E-03	3.60E-01	7.94E-03
M1224_1.01	Gap-box_motif	9	3	7	11	9	4	19	6	1.62E-02	7.65E-01	1.83E-01
M0758_1.01	M1561_1.01	80	71	62	78	71	81	43	54	1.87E-02	6.99E-01	−5.21E-02
MYB3_binding_site motif	M0758_1.01	25	34	40	41	44	21	20	35	2.02E-02	3.88E-03	−2.17E-01

Motif pairs with pronounced non-random motif order and orientation preferences (motif-pair arrangement). Motif pairs were considered in both relative positions (motif 1 upstream of motif 2 or the reverse). For both arrangements, four different motif combinations of motif orientations are possible with “+”/”-“denoting forward and reverse-complement direction, respectively. P_BHEntropy is the multiple-testing corrected p-value obtained from testing the significance of the motif order and orientation entropy (see Methods). P_BHExpr is the p-value of the detected co-expression difference of genes associated with the most frequent arrangement relative to the three least frequent arrangements. Cohen’s d refers to the associated effect size with positive signs signifying increased co-expression among genes harboring the most frequent arrangement relative to the genes harboring the three least frequent arrangements. Motif pairs with 50 or more occurrences were considered only. Zero values of P_BHEntropy indicate that the empirical p-value was below the limit of the shuffling repetitions (see Methods). For the MYB1_binding_site motif, insufficient gene expression information was available for the set of unique genes in which the pair was found. Note that for same-pair motifs, order is irrelevant and only four arrangements were considered

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