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Table 2 Motif synergy groups from up-regulated genes

From: Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors

Transcription Factor(s)a EC scoreb Threshold EC scorec No. of genesd
WRKY 0.22 0.18 9
TCP2 1 0.16 3
NAC, WRKY, DOF 0.27 0.2 6
NAC, HSF, WRKY 0.22 0.17 10
NAC, HSF, DOF 0.23 0.22 20
NAC, AP2(CBF), WRKY, DOF 0.25 0.17 8
NAC, AP2(CBF), WRKY 0.27 0.2 6
NAC, AP2(CBF), HSF, WRKY 0.24 0.17 13
NAC, AP2(CBF), HSF, DOF 0.18 0.17 11
NAC, AP2(CBF), HSF 0.26 0.18 25
MYB, NAC 0.56 0.17 10
MYB, MADS 1 0.16 3
MYB, DOF 0.52 0.21 34
MYB, BZIP, DOF 0.33 0.16 3
MYB, BZIP, BHLH, NAC, DOF 0.33 0.16 3
MYB, BZIP 1 0.17 4
MYB, BHLH, NAC, DOF 0.47 0.2 6
MYB, BHLH, NAC 0.36 0.17 11
MYB, BHLH, MADS 1 0.16 3
MYB, BHLH, DOF 0.33 0.18 14
MYB, BHLH 0.69 0.17 10
MYB 0.59 0.2 19
MADS, DOF 0.8 0.2 5
MADS 1 0.17 8
HSF, WRKY, DOF 0.36 0.17 8
HSF, WRKY 0.22 0.18 9
HSF 0.21 0.2 28
DOF 0.23 0.19 122
BZIP, WRKY, DOF 0.33 0.17 4
BZIP, NAC, HSF 0.33 0.16 3
BZIP, NAC, AP2(CBF), HSF, WRKY, DOF 0.33 0.16 3
BZIP, NAC, AP2(CBF), HSF 0.33 0.16 3
BZIP, NAC, AP2(CBF), DOF 0.4 0.2 5
BZIP, NAC, AP2(CBF) 0.67 0.16 3
BZIP, DOF 0.22 0.18 9
BZIP, BHLH, NAC, DOF 0.67 0.16 3
BZIP, BHLH 0.44 0.18 9
BZIP 0.52 0.21 33
BHLH, NAC, DOF 0.27 0.22 21
BHLH, NAC 0.38 0.2 19
BHLH, MADS, DOF 1 0.16 3
BHLH, DOF 0.49 0.21 34
BHLH 0.45 0.21 35
AP2(CBF), HSF, DOF 0.19 0.18 16
AP2(CBF), HSF 0.23 0.2 32
AP2(CBF), DOF 0.27 0.17 11
AP2(CBF) 0.27 0.2 6
AP2(AtERF), HSF, WRKY 0.33 0.16 3
AP2(AtERF), DOF 0.5 0.17 4
  1. Results obtained by applying the method using the confidence interval criterion on the genes filtered from the 24 k gene array data set. a: TF families. b: EC score obtained from the cluster of putative target genes predicted by this method. c: Threshold above which the EC score is acceptable. d: Number of putative target genes that are regulated by the TF families that are indicated in the first column.