Table 2

Gene ontology analyses of down-regulated genes

Non-redundant GO categories

Level

Differentially

expressed (%)

Total genes in

the class (%)

P


Over-represented

Photosynthesis

3

4.76 (16)

0.57

5.99×10-7

Response to jasmonic acid stimulus

4

3.79 (12)

0.98

8.94×10-3

Response to salicylic acid stimulus

4

3.15 (10)

0.89

3.70×10-2

Response to auxin stimulus

5

8.77 (25)

2.06

2.14×10-6

Response to salt stress

5

5.61 (16)

1.41

7.85×10-4

Response to water deprivation

5

4.21 (12)

0.87

1.59×10-3

Response to ethylene stimulus

5

4.21 (12)

1.23

1.97×10-2

Response to cadmium ion

6

3.95 (9)

0.44

3.67×10-4

Lipids biosynthetic processes

6

9.21 (21)

3.11

1.59×10-3

Chloroplast organization and biogenesis

6

2.63 (6)

0.36

1.84×10-2

Chlorophyll biosynthesis

7

4.52 (8)

0.20

1.03×10-5

Vitamin E biosynthesis

7

2.26 (4)

0.05

1.72×10-3

Abscisic acid mediated signaling

7

3.95 (7)

0.60

1.13×10-2

NADH dehydrogenase complex assembly

8

1.89 (2)

0.00

3.70×10-2

Starch biosynthetic processes

9

7.14 (4)

0.34

1.12×10-2

Tetraterpenoid metabolism

9

8.93 (5)

1.17

3.79×10-2


Non-redundant GO categories identified as enriched among up-regulated genes in infected plants versus mock-inoculated plants. The percentages of genes belonging to each category are reported for the differentially expressed genes and for the A. thaliana genes present in the microarray. The absolute number of genes is reported in parenthesis for the differentially expressed set. P: FDR-corrected P-value for the Fisher's exact test in a 2 × 2 contingency table.

Agudelo-Romero et al. Virology Journal 2008 5:92   doi:10.1186/1743-422X-5-92

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