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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.

From: Tissue-specific mRNA expression profiling in grape berry tissues

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)
  1. 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.
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