Skip to main content

Table 2 Functional categories of the differentially expressed (p ≤ 0.05, 2-fold) mRNA among berry tissues from well-watered vines

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

Functional category % of Unigenes over expressed in: % of Unigenes under expressed in: % total in probesets
a) Top level Pulp Skin Seed Pulp Skin Seed  
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)
b) Metabolism        
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)
  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 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.
\