|
Functional categories of the differentially expressed (p ≤ 0.05, 2-fold) mRNA among berry tissues from well-watered vines |
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| Functional category |
% of Unigenes over expressed in: |
% of Unigenes under expressed in: |
% total in probesets |
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|
|
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| a) Top level |
Pulp |
Skin |
Seed |
Pulp |
Skin |
Seed |
|
|
|
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| Protein with binding function |
27.0 (64) |
20.1 (154) |
25.0 (269) |
21.9 (195) |
26.7 (52) |
24.8 (281) |
26.3 (3588) |
| Metabolism |
27.0 (64) |
31.5 (241) |
27.4 (295) |
31.9 (284) |
28.2 (55) |
25.7 (291) |
20.9 (2851) |
| Protein fate |
16.0 (38) |
12.2 (93) |
17.2 (185) |
12.4 (110) |
22.0 (43) |
16.3 (185) |
16.7 (2270) |
| Signal transduction mechanism |
13.5 (32) |
15.7 (120) |
11.0 (118) |
11.7 (104) |
15.9 (31) |
18.4 (209) |
13.6 (1847) |
| Transcription |
15.2 (36) |
13.2 (101) |
13.7 (148) |
11.5 (102) |
11.8 (23) |
16.1 (183) |
12.9 (1762) |
| Cell rescue, defense and virulence |
10.5 (25) |
17.4 (133) |
15.7 (169) |
15.5 (138) |
14.4 (28) |
12.9 (146) |
11.1 (1509) |
| Development |
13.9 (33) |
11.8 (90) |
12.1 (130) |
9.5 (85) |
9.7 (19) |
13.2 (150) |
11.8 (1611) |
| Cell fate |
12.6 (30) |
8.6 (66) |
9.4 (101) |
8.5 (76) |
10.3 (20) |
10.3 (117) |
11.7 (1593) |
| Control of cellular organization |
10.6 (25) |
10.1 (77) |
9.7 (105) |
10.0 (89) |
9.2 (18) |
10.6 (120) |
9.5 (1296) |
| Interaction with cellular environment |
10.1 (24) |
8.4 (64) |
11.4 (123) |
8.8 (78) |
13.8 (27) |
8.8 (100) |
8.5 (1158) |
| Cell cycle and DNA processing |
8.4 (20) |
4.4 (34) |
7.6 (82) |
3.9 (35) |
11.3 (22) |
7.0 (80) |
8.4 (1145) |
| Transport facilitation |
7.2 (17) |
15.6(119) |
10.6 (114) |
15.4 (137) |
11.3 (22) |
9.3 (106) |
8.6 (1174) |
| Cellular transport |
9.3 (22) |
6.3 (48) |
5.6 (60) |
6.8 (60) |
5.1 (10) |
8 (91) |
7.2 (982) |
| Protein synthesis |
3.8 (9) |
2.6 (20) |
8.1 (87) |
7.6 (68) |
5.1 (10) |
3.4 (39) |
7.5 (1017) |
| Energy |
4.6 (11) |
11.0 (84) |
8.4 (91) |
11.9 (106) |
9.2 (18) |
6.9 (78) |
7.0 (947) |
| Interaction with environment |
8.9 (21) |
7.8 (60) |
9.3 (100) |
6.6 (59) |
11.3 (22) |
8.9 (101) |
7.0 (956) |
| Protein activity regulation |
4.6 (11) |
2.3 (18) |
3.0 (32) |
2.5 (22) |
6.7 (13) |
2.6 (29) |
3.5 (478) |
| Cell type differentiation |
3.0 (7) |
2.0 (15) |
2.1 (23) |
1.6 (14) |
2.6 (5) |
1.8 (21) |
1.9 (257) |
| Storage protein |
0 (0) |
0 (0) |
0.7 (8) |
0.1 (1) |
0 (0) |
0.1 (1) |
0.3 (45) |
| Unknown function |
16.9 (40) |
11.0 (84) |
11.0 (118) |
11.5 (102) |
14.4 (28) |
13.5 (153) |
9.6 (1306) |
| No hit |
24.1 (57) |
21.2 (162) |
26.4 (284) |
22.6 (201) |
28.7 (56) |
21.5 (244) |
34.2 (4656) |
|
|
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| b) Metabolism |
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| Carbohydrates |
14.8 (35) |
12.9 (99) |
11.0 (118) |
12.1 (108) |
7.7 (15) |
11.3 (128) |
8.6 (1169) |
| Secondary metabolism |
9.3 (22) |
9.4 (72) |
8.7 (93) |
10.4 (93) |
8.2(16) |
6.5 (74) |
4.8 (652) |
| Lipids |
3.4 (8) |
8.4 (64) |
5.8 (62) |
8.5 (76) |
4.6 (9) |
5 (57) |
4.6 (632) |
| Amino acids |
1.7 (4) |
6.5 (50) |
6.3 (68) |
7.4 (66) |
6.7 (13) |
4.9 (55) |
3.8 (511) |
| Vitamins and cofactors |
3.8 (9) |
3.9 (30) |
3.3 (36) |
5.4 (48) |
1.5 (3) |
2.4 (27) |
2.4 (326) |
| Phosphate |
3.4 (8) |
4.3 (33) |
2.7 (29) |
2.1 (19) |
4.6 (9) |
4.3 (49) |
3.2 (433) |
| Nucleotides |
4.6 (11) |
2.6 (20) |
3.5 (38) |
3.7 (33) |
3.1 (6) |
2.7 (31) |
2.9 (401) |
| Nitrogen and sulfur |
0.4 (1) |
1.8 (14) |
3.1 (33) |
3.3 (29) |
3.6 (7) |
1.3 (15) |
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 ompared 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 |
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