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Table 3 Motif pair co-occurrence statistics

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

Motif 1 Motif 2 Genes with motif 1 Genes with motif 2 Genes with both motifs p-value (BH corrected) pBH 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
  1. Motif pairs found to co-occur more often than expected in the same upstream regions (pBH, 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. PBHExpr 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