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Table 7 ChIP-Seq and RNA-Seq data reveals genes potentially regulated by YABBY transcription factor

From: Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq

  

Stage 3

Stage 6

   

Gene model

Motif

(RPKM)

(RPKM)

Regulation

P-value

Annotation

Glyma01g03500.1

Motif2

1.4

4.05

Up

0.000246

Kelch motif containing protein

Glyma01g05750.1

Motif2

21.2

9.3

Down

0.014209

GDA1 nucleoside phosphatase

Glyma01g34490.1

Motif2

1.6

0.08

Down

4.41E-06

HSF-type DNA-binding protein

Glyma02g03890.1

Motif1,3

4.1

0.22

Down

2.69E-15

Armadillo/beta-catenin-like repeat

Glyma02g08840.1

Motif1

22.8

3.08

Down

6.59E-13

AP2 domain containing protein

Glyma02g35550.1

Motif2

1.7

4.5

Up

3.00E-07

Protein tyrosine kinase

Glyma03g39930.1

Motif3

14.6

8.2

Down

0.042524

Signal peptidase

Glyma04g33270.1

Motif2

0.70

0.13

Down

0.030654

No apical meristem (NAM) protein

Glyma05g36070.1

Motif1

4.7

1.8

Down

0.000671

GCC2 and GCC3

Glyma06g13910.1

Motif2

1.07

2.1

Up

0.00103

Auxin responsive protein

Glyma07g18350.1

Motif1

10.1

2.07

Down

0.000109

Fatty acid desaturase

Glyma08g19270.1

Motif3

21.3

6.01

Down

0.000737

Protein tyrosine kinase

Glyma10g38770.1

Motif3

0.66

2.4

Up

1.69E-11

PAZ domain containing protein

Glyma11g04900.1

Motif2

4.6

1.8

Down

0.020018

Leucine Rich Repeat protein

Glyma11g04950.1

Motif2

2.8

0.44

Down

0.009353

ACT domain containing protein

Glyma11g05920.1

Motif1

9.2

2.7

Down

0.000165

HLH DNA-binding domain protein

Glyma12g32590.1

Motif1

0.38

4.5

Up

2.05E-14

No Functional Annotation

Glyma12g32690.1

Motif1

49.4

0.9

Down

1.50E-36

No Functional Annotation

Glyma13g00380.1

Motif3

10.1

1.4

Down

3.36E-06

WRKY DNA -binding domain

Glyma13g00840.1

Motif1

18.3

2.8

Down

6.31E-11

E1-E2 ATPase

Glyma13g28450.1

Motif1

5.9

1.5

Down

2.03E-08

Sugar transporter

Glyma13g31010.1

Motif2

15.1

0.50

Down

4.31E-25

AP2 domain containing protein

Glyma14g36810.1

Motif2

1.6

3.4

Up

7.07E-05

lectin domain containing protein

Glyma15g13830.1

Motif3

38.1

13.8

Down

3.10E-05

GTPase of unknown function

Glyma18g02280.3

Motif3

1.3

4.2

Up

0.000148

No Functional Annotation

Glyma18g42700.1

Motif2

3.9

0.08

Down

2.26E-15

Protein tyrosine kinase

Glyma19g32880.1

Motif1

11.8

0.72

Down

7.91E-23

Cytochrome P450

Glyma20g03420.1

Motif2

8.06

2.3

Down

7.47E-06

GC-rich DNA-binding factor protein

Glyma20g04490.1

Motif2

17.6

16.5

Down

0.016291

lipoprotein A (RlpA)-like protein

Glyma20g24990.2

Motif2

54.5

128.6

Up

2.88E-06

No Functional Annotation

  1. Complete table can be found in Additional file 4.
  2. Binding motif number refer to those listed in Table 5. P-values were calculated by the DESeq package using the hit number from RNA-Seq libraries.
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