Table 3

Functional categories of the differentially expressed (p ≤ 0.05, 2-fold) mRNA between pulp and skin from well-watered and water-deficit treated vines.

Functional category

% Unigenes over expressed in pulp:

% Unigenes over expressed in skin:

% Unigenes over expressed in seed:

% total in probesets

a) Top level

Well-watered

Water-deficit

Well-watered

Water-deficit

Well-watered

Water-deficit

Protein with binding function

19.8 (23)

11.0 (12)

10.2 (13)

11.9 (18)

17.5 (7)

10.3 (3)

29.5 (5994)

Metabolism

37.9 (44)

28.4 (31)

23.4 (30)

41.7 (63)

42.5 (17)

6.9 (2)

20.9 (2851)

Protein fate

8.6 (10)

6.4 (7)

8.6 (11)

5.3 (8)

15 (6)

0 (0)

16.7 (2270)

Signal transduction mechanism

12.9 (15)

9.2 (10)

8.6 (11)

9.9 (15)

10 (4)

6.9 (2)

13.6 (1847)

Transcription

7.8 (9)

10.1 (11)

11.7 (15)

7.3 (11)

5 (2)

6.9 (2)

12.9 (1762)

Cell rescue, defense and virulence

21.5 (25)

18.3 (20)

11.7 (15)

18.5 (28)

22.5 (9)

10.3 (3)

11.1 (1509)

Development

12.9 (15)

7.3 (8)

10.9 (14)

3.3 (5)

12.5 (5)

3.4 (1)

11.8 (1611)

Cell fate

6.0 (7)

5.5 (6)

5.5 (7)

4.6 (7)

5 (2)

0 (0)

11.7 (1593)

Control of cellular organization

6.9 (8)

6.4 (7)

9.4 (12)

10.6 (16)

10 (4)

10.3 (3)

9.5 (1296)

Interaction with cellular environment

12.1 (14)

3.7 (4)

14.1 (18)

4.6 (7)

10 (4)

6.9 (2)

8.5 (1158)

Cell cycle and DNA processing

3.4 (4)

1.8 (2)

1.6 (2)

3.3 (5)

0 (0)

0 (0)

8.4 (1145)

Transport facilitation

19.8 (23)

8.3 (9)

13.3 (17)

7.9 (12)

12.5 (5)

3.4 (1)

8.6 (1174)

Cellular transport

8.6 (10)

1.8 (2)

4.7 (6)

4.0 (6)

0 (0)

0 (0)

7.2 (982)

Protein synthesis

1.7 (2)

2.7 (3)

2.3 (3)

4.0 (6)

10 (4)

0 (0)

7.5 (1017)

Energy

14.7 (17)

9.2 (10)

10.2 (13)

10.6 (16)

22.5 (9)

0 (0)

7.0 (947)

Interaction with environment

12.1 (14)

9.2 (10)

7.8 (10)

9.9 (15)

5 (2)

0 (0)

7.0 (956)

Protein activity regulation

1.7 (2)

0 (0)

3.1 (4)

0.7 (1)

2.5 (1)

0 (0)

3.5 (478)

Cell type differentiation

1.7 (2)

0 (0)

2.3(3)

0 (0)

0 (0)

0 (0)

1.9 (257)

Storage protein

0 (0)

0.9 (1)

0 (0)

0 (0)

0 (0)

6.9 (2)

0.3 (45)

Unknown function

13.8 (16)

5.5 (6)

14.8 (19)

13.9 (21)

2.5 (1)

10.3 (3)

9.6 (1306)

No hit

14.7 (17)

38.5 (42)

22.7 (29)

23.2 (35)

30 (12)

58.6 (17)

34.2 (4656)

b) Metabolism

Carbohydrates

19.8 (23)

11.9 (13)

13.3 (17)

17.9 (27)

17.5 (7)

6.9 (2)

8.6 (1169)

Secondary metabolism

13.8 (16)

12.8 (14)

9.4 (12)

22.5 (34)

15 (6)

0 (0)

4.8 (652)

Lipids

10.3 (12)

7.3 (8)

3.9 (5)

6.0 (9)

10 (4)

0 (0)

4.6 (632)

Amino acids

6.9 (8)

3.7 (4)

5.5 (7)

7.3 (11)

7.5 (3)

0 (0)

3.8 (511)

Vitamins and cofactors

5.2 (6)

2.7 (3)

2.3 (3)

4.6 (7)

5 (2)

0 (0)

2.4 (326)

Phosphate

0.9 (1)

1.8 (2)

0 (0)

0 (0)

2.5 (1)

0 (0)

3.2 (433)

Nucleotides

4.3 (3)

2.7 (3)

3.9 (3)

3.3 (4)

7.5 (3)

0 (0)

2.9 (401)

Nitrogen and sulfur

4.6 (5)

2.6 (3)

3.3 (5)

3.9 (5)

7.5 (3)

0 (0)

1.4 (184)

Unigenes were grouped according to Figure 1. The functional categories were assigned according to the MIPS functional catalog as a) top level categories and b) second level categories within the metabolism category. The values in parentheses correspond to the total number of Unigenes observed in each category. The last column corresponds to the relative percentage within each category of all 13,622 Unigenes present on the Vitis Genechip® genome array. Typefaces indicate functional categories that are significantly over- (bold) or under- (italic) represented when compared to the overall distribution of all 13,622 Unigenes using a Fisher's exact test. Underscores indicate over- or under-representation, respectively, of more than 1.5-fold the percentage expected in that category based on the overall distribution of all Vitis Unigenes.

Grimplet et al. BMC Genomics 2007 8:187   doi:10.1186/1471-2164-8-187

Open Data