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

BMC Genomics

Table 3 Motif pair co-occurrence statistics

Motif 1	Motif 2	Genes with motif 1	Genes with motif 2	Genes with both motifs	p-value (BH corrected)	p_BH Expr	Cohen’s d
M0758_1.01	Bellringer/replumless/pennywise_BS1_IN_AG	6845	6630	1619	0.00E + 00	1.00E + 00	6.51E-03
TELO-box_promoter motif	TELO-box_promoter motif	1472	1472	146	0.00E + 00	3.03E-42	2.82E-01
SBOXATRBCS	M0769_1.01	276	2106	45	2.61E-06	1.00E + 00	−1.58E-02
M2220_1.01	M2220_1.01	213	213	12	5.86E-06	1.00E + 00	1.04E-01
M0758_1.01	ATHB6_binding_site motif	6845	666	187	3.92E-04	1.31E-01	−1.13E-02
Bellringer/replumless/pennywise_BS1_IN_AG	M2241_1.01	6630	2342	555	3.92-04	1.00E + 00	2.01E-03
Bellringer/replumless/pennywise_BS1_IN_AG	ATHB6_binding_site motif	6630	666	180	8.79E-04	1.00E + 00	−1.56E-02
MYB1_binding_site motif	SBOXATRBCS	912	276	22	1.55E-03	1.00E + 00	−3.43E-02
M0758_1.01	SORLREP3	6845	1520	376	4.49E-03	5.17E-01	7.62E-03
EveningElement_promoter motif	Bellringer/replumless/pennywise_BS1_IN_AG	1249	6630	305	5.61E-03	2.21E-03	2.51E-02
ATHB6_binding_site motif	M2241_1.01	666	2342	74	8.86E-03	1.00E + 00	1.82E-02
M0758_1.01	M2241_1.01	6845	2342	552	1.42E-02	1.74E-01	−6.70E-03
TELO-box promoter motif	TL1ATSAR	1472	85	12	4.01E-02	1.00E + 00	3.22E-01

Motif pairs found to co-occur more often than expected in the same upstream regions (p_{BH, hypergeometric} <0.05, where BH denotes correction for multiple testing based on Benjamini-Hochberg [48]). Co-occurrences were counted only if motifs were found not to overlap with regard to their mapping position. P_BHExpr is the p-value of the detected co-expression difference of genes containing both motifs compared to those containing only one of them in their upstream region with Cohen’s d referring to the associated effect size. Motif pairs with more than five co-occurrences are reported only. In case of same-pair motifs, genes with the respective motif found repeatedly in their upstream sequence were compared to genes harboring the motif only once

ISSN: 1471-2164