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Table 4 Plant transcription factor binding sites significantly ( P <0.05) overrepresented in the promoters of HD-Zip genes belonging to each of the subfamilies

From: Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress

 

Motif #

1TFBS

2Count

3Proportion

4TFBS_Dehydration

5TFBS_Salt

6TF_Class

7DE_Dehydration

8DE_Salt

HD-Zip I

M00354

Dof3

33

91.7

-

-

Dof

+

+

 

M00700

ROM

31

86.1

+

-

bZIP

+

+

 

M01136

Dof

29

80.6

-

-

Dof

+

+

 

M00353

Dof2

27

75.0

-

-

Dof

+

+

9HD-Zip II

M00479

Alfin1

21

91.3

-

-

PHD

+

+

 

M01136

Dof

20

87.0

-

-

Dof

+

+

 

M00354

Dof3

19

82.6

-

-

Dof

+

+

 

M00440

CG1

18

78.3

-

-

CAMTA

+

+

 

M00506

LIM1

18

78.3

-

-

LIM

-

+

 

M00502

TEIL

17

73.9

-

+

10AP2-EREBP

+

+

 

M00653

OCSBF-1

17

73.9

+

+

bZIP

+

+

 

M00788

EmBP-1b

17

73.9

+

+

bZIP

+

+

 

M01128

SED

17

73.9

-

-

DOF

+

+

 

M00942

CPRF-1

16

69.6

+

-

bZIP

+

+

 

M00948

PCF2

16

69.6

+

-

TCP

+

+

 

M00443

Opaque-2

14

60.9

+

+

bZIP

+

+

 

M01133

AG

14

60.9

-

-

MADS

+

+

 

M00660

RITA-1

13

56.5

+

+

bZIP

+

+

 

M01130

PBF

13

56.5

-

-

Dof

+

+

 

M01054

bHLH66

12

52.2

+

+

bHLH

+

+

 

M00503

ATHB-5

11

47.8

+

-

HD-Zip I

+

+

 

M00434

PIF3

10

43.5

+

+

bHLH

+

+

HD-Zip III

M00479

Alfin1

10

90.9

-

-

PHD

+

+

 

M00438

ARF

9

81.8

-

-

ARF

+

+

 

M01021

ID1

9

81.8

+

-

C2H2 - zinc

+

+

 

M01126

BPC1

8

72.7

-

-

BBR/BPC

-

-

 

M00948

PCF2

7

63.6

+

-

TCP

+

+

 

11M00151

AG

7

63.6

-

-

MADS

+

+

 

M00820

HAHB-4

6

54.5

-

-

HD-Zip I

+

+

 

12M01061

AGL2

6

54.5

-

-

MADS

+

+

 

M00392

AGL3

5

45.5

-

-

MADS

+

+

 

M00949

AGL15

5

45.5

-

-

MADS

+

+

HD-Zip IV

13M00355

PBF

29

96.7

+

-

Dof

+

+

 

M00438

ARF

25

83.3

-

-

ARF

+

+

 

M01126

BPC1

25

83.3

-

-

BBR/BPC

-

-

 

M01136

Dof

25

83.3

-

-

Dof

+

+

 

M01128

SED

23

76.7

-

-

DOF

+

+

 

M01021

ID1

22

73.3

+

-

C2H2 - zinc

+

+

 

M00702

SPF1

20

66.7

-

+

10WRKY

+

+

 

M00654

OSBZ8

15

50.0

+

+

bZIP

+

+

 

M00089

Athb-1

11

36.7

+

-

HD-Zip I

+

+

  1. 1TFBS: Transcription factor binding site (TFBS) significantly (P <0.05, motif score >5) overrepresented in the promoters of HD-Zip genes.
  2. 2Count: Number of HD-Zip genes within a subfamily that contain the TFBS significantly overrepresented in their promoters.
  3. 3Proportion: Percentage of HD-Zip genes within a subfamily that contain the TFBS overrepresented in their promoters.
  4. 4TFBS_Dehydration: " + " indicates that the respective TFBS is overrepresented in the promoters of genes that were differentially expressed under dehydration stress, and "-" represents not overrepresented.
  5. 5TFBS_Salt: " + " indicates that the respective TFBS is overrepresented in the promoters of genes that were differentially expressed under salt stress, and "-" represents not overrepresented.
  6. 6TF_Class: The membership of TFBS to a particular transcription factor (TF) class based on TRANSFAC [72] and UniprotKB [134].
  7. 7DE_Dehydration: " + " indicates members of the respective TF class are differentially expressed (DE) under dehydration stress, and “-” indicates otherwise.
  8. 8DE_Salt: " + " indicates members of the respective TF class are DE under salt stress, and “-” indicates otherwise.
  9. 9Although the HD-Zip II subfamily has 24 genes, the proportion is calculated using 23 genes. HD-Zip II gene Glyma05g23150 was excluded from the promoter analysis due to the selection criteria utilized (see methods for promoter selection criteria).
  10. 10TF class significantly (corrected P <0.05) overrepresented in the DE genes under dehydration and salt stress.
  11. 11AG TFBS has multiple motif identifiers - M00151, M01063, M01133, and M00950. Counts of AG TFBS’s irrespective of the identifier# were summed to estimate total count and proportion.
  12. 12AGL2 TFBS has two motif identifiers - M01061 and M01062. Counts of AGL2 TFBS’s irrespective of the identifier# were summed to estimate total count and proportion.
  13. 13PBF TFBS has two motif identifiers - M00355 and M01130. Counts of PBF TFBS’s irrespective of the identifier# were summed to estimate total count and proportion.
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BMC Genomics

ISSN: 1471-2164

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