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Table 4 Motif pairs with pronounced motif order 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 pBH Binom pBH Expr Cohen’s d
++ +− -- −+ ++ +− -- −+
M2217_1.01 M0758_1.01 53 60 49 39 99 65 67 77 2.44E-04 4.32E-01 −1.81E-02
M2217_1.01 M2241_1.01 17 12 16 6 32 23 18 36 2.66E-04 4.32E-01 −5.83E-02
Gap-box motif TELO-box_promoter motif 30 10 43 11 8 12 18 5 5.28E-04 3.78E-01 −6.42E-02
Bellringer/replumless/pennywise_BS1_IN_AG M2241_1.01 89 70 79 78 97 88 99 134 4.77E-03 3.78E-01 −3.05E-02
M0758_1.01 SORLREP3 77 64 79 74 48 66 51 55 2.12E-02 3.78E-01 2.90E-02
M0769_1.01 MYB1_binding_site motif 22 12 8 7 7 3 4 7 2.12E-02 7.67E-01 −3.65E-02
M2241_1.01 M1224_1.01 4 4 8 5 9 12 14 13 2.24E-02 7.58E-01 1.17E-02
Bellringer/replumless/pennywise_BS1_IN_AG M2251_1.01 35 25 22 23 28 9 13 14 2.25E-02 7.58E-01 2.62E-02
M2251_1.01 M1561_1.01 5 4 5 6 16 7 6 17 2.25E-02 7.58E-01 −4.86E-02
TELO-box_promoter motif Bellringer/replumless/pennywise_BS1_IN_AG 32 29 32 26 40 41 44 45 3.23E-02 1.37E-02 −1.14E-01
M0758_1.01 M2251_1.01 39 36 25 22 27 25 19 9 3.30E-02 7.20E-01 8.89E-04
SORLREP3 M2241_1.01 20 13 10 17 32 23 20 22 3.30E-02 4.08E-01 3.15E-02
  1. Motif pairs with pronounced motif order preferences. 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. PBHBinom is the multiple-testing corrected p-value obtained from testing the order preference based on binomial test with p = 0.5 as the assumed background probability (no preferred motif order) and based on the summed up counts (over all four orientation arrangements) for the two motif orders respectively. PBHExpr is the p-value of the detected co-expression difference of genes in which the motif pair was found in one order relative to genes with the inverse motif order (genes found in both sets were excluded). Cohen’s d refers to the associated effect size with positive signs signifying increased co-expression among genes with motif order 1–2, negative signs among genes with motif order 2–1. Motif pairs with 50 or more occurrences were considered only. Note that for same-motif pairs, this analysis has no meaning, hence they were not considered