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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.