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Table 2 Regulated transcription factors during CIM and SIM

From: Genome scale transcriptome analysis of shoot organogenesis in Populus

  

NO.

NO.

B vs. A

C vs. A

D vs. A

E vs. A

Gene family

Percentage

(regulated)

(total)

Up

Down

Up

Down

Up

Down

Up

Down

SRS

80.0%

8

10

3

 

5

 

2

 

4

 

TLP

72.7%

8

11

 

6

4

4

2

6

2

4

AUX-IAA

69.7%

23

33

9

11

2

16

 

27

 

15

CCAAT-HAP2

45.5%

5

11

 

5

 

2

 

4

 

4

GRF

44.4%

4

9

      

4

 

C2C2-Dof

42.9%

18

42

5

11

 

13

3

13

 

14

WRKY

38.5%

40

104

22

12

27

14

29

14

25

10

ARF

37.8%

14

37

 

13

 

10

 

13

 

10

HB

37.7%

40

106

15

23

7

22

7

24

6

24

AS2

36.8%

21

57

8

4

15

2

8

4

6

3

FHA

36.8%

7

19

 

7

 

8

 

4

 

4

ZIM

36.4%

8

22

8

3

7

2

5

3

4

2

GARP-G2-like

35.8%

24

67

2

19

4

14

6

19

3

15

TCP

35.3%

12

34

 

11

2

9

 

9

3

8

HMG

33.3%

4

12

2

2

2

2

2

3

2

3

LIM

33.3%

7

21

 

7

 

7

 

7

 

7

ULT

33.3%

1

3

  

1

 

1

 

1

 

ZF-HD

32.0%

8

25

 

6

 

4

 

3

2

 

E2F-DP

30.0%

3

10

2

2

      

SBP

27.6%

8

29

 

8

4

5

 

7

 

6

CCAAT-HAP3

26.3%

5

19

 

5

 

3

 

3

 

3

Trihelix

25.5%

12

47

4

6

4

4

5

4

4

3

bHLH

25.0%

37

148

9

25

5

27

5

24

4

19

PLATZ

25.0%

5

20

5

4

4

2

3

2

3

2

bZIP

22.4%

19

85

4

22

2

18

4

17

3

17

Alfin

22.2%

2

9

 

2

      

GRAS

20.8%

20

96

7

12

5

7

8

12

5

7

MYB-related

20.2%

17

84

5

14

3

6

2

7

2

6

HSF

19.4%

6

31

7

 

11

 

7

 

5

 

MYB

19.0%

41

216

13

27

11

27

12

29

11

27

AP2-EREBP

18.9%

40

212

28

10

23

8

25

8

25

 

NAC

18.6%

32

172

16

15

10

13

6

15

7

13

C2C2-CO-like

17.9%

7

39

 

10

 

6

 

7

 

5

C3H

17.9%

14

78

10

3

9

2

7

5

6

2

PcG

17.8%

8

45

2

6

2

3

 

3

 

2

C2H2

16.0%

13

81

5

11

3

9

3

9

2

9

C2C2-GATA

15.6%

5

32

 

2

 

2

3

3

  

C2C2-YABBY

15.4%

2

13

      

3

 

JUMONJI

15.0%

3

20

    

2

   

TAZ

14.3%

1

7

   

1

 

1

  

GARP-ARR-B

13.3%

2

15

 

4

  

2

3

 

3

ABI3-VP1

11.1%

12

108

9

4

9

2

10

2

9

6

MADS

10.8%

12

111

 

8

2

7

6

5

2

6

CCAAT-HAP5

10.5%

2

19

    

2

 

2

 

PHD

9.3%

8

86

7

3

5

 

3

2

4

2

Total

22.8%

588

2576

        
  1. The JGI gene model IDs were downloaded from the Database of Poplar Transcription Factors (DPTF) and were searched against the list of the differentially expressed genes identified by LIMMA. The list is ranked by the percentage of the total number of each transcription factor class in poplar. The total number of regulated transcription factors were corrected for redundancy among the array probes; the number of up-or down-regulated transcription factors at each stage were not corrected for redundancy (i.e., multiple probe sets targeting the same transcript may be present).
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BMC Plant Biology

ISSN: 1471-2229

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