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Table 1 Gene onotology (GO) enrichment analysis for genes exhibiting significant presence-absence expression variation (PAV) (FDR<0.001). GO enrichment was conducted using AgriGO using the MSU V7 genome build without transposable elements as a background. GO enrichment was conducted separately for genes expressed predominately in each subspecies

From: Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

Subspecies

Ont. Cat.

GO Description

No. in input

No. in background

p-value

FDR

Japonica

P

response to stress

137

4660

1.5×1−10

5.2×1−8

 

P

response to stimulus

172

6928

1.0×1−7

1.7×1−5

 

P

response to biotic stim.

43

1404

2.4×1−4

2.7×1−2

 

F

oxygen binding

25

390

5.0×1−8

4.5×1−6

 

F

nucleotide binding

92

3490

2.4×1−5

1.1×1−3

 

F

transferase activity

120

5200

3.6×1−4

9.6×1−3

 

F

catalytic activity

271

13508

4.2×1−4

9.6×1−3

 

F

kinase activity

69

2699

6.4×1−4

9.6×1−3

Indica

F

oxygen binding

13

390

1.5×1−4

8.8×1−3