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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 pBH Entropy pBH 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
  1. 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. PBHEntropy is the multiple-testing corrected p-value obtained from testing the significance of the motif order and orientation entropy (see Methods). PBHExpr 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 PBHEntropy 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