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Table 2 RY repeat motifs enriched in the 5’-regulatory regions of 47 PR genes, particularly in 9 chitinase genes, which were up-regulated in IR28 and suppressed in LYP9

From: Differential expression profiling of the early response to Ustilaginoidea virens between false smut resistant and susceptible rice varieties

Motif_seq

PR genes (47)

Chitinase (9)

PR genes (660)

Protein kinases (52)

Annotation

Motif_ID

Numa

RARb

P_value

Num

RAR

P_value

Num

RAR

P_value

Num

RAR

P_value

CATGCATG

31

6.3387

8.89E-13

11

11.7459

3.85E-07

174

2.5336

8.03E-24

6

1.1089

0.8205

RY repeat motif

S000102

CATGCAT

55

5.1483

1.15E-15

16

7.8213

6.97E-07

337

2.2464

4.15E-31

14

1.1845

0.5290

RY repeat motif

S000105

CATGCAY

69

4.4198

3.05E-15

19

6.3557

2.10E-06

462

2.1074

2.07E-33

20

1.1579

0.5860

RY repeat motif

S000100

CATGCA

92

3.5564

2.15E-13

25

5.0468

7.38E-06

700

1.9270

6.24E-34

28

0.9783

1.0000

RY repeat motif

S000264

  1. aThe number of RY repeat motifs
  2. bRAR = (motif count in a selected promoter set/number of promoters in the set)/(motif count in total promoters/number of total promoters)
  3. P values were calculated using Fisher’s exact test
  4. The total set of sequence-available PR genes (660) and that 52 protein kinase genes that were up-regulated in IR28 were used for comparisons