Table 2.

Distribution of the Functional Classes of Genes in Maize Whole Genome as Well as in Endosperm-Specific and Tomato Genome-Wide ESTs

No.
Category
Whole maize genome ESTsa
Total maize endosperm ESTsb
Novel maize endosperm ESTsc
Whole tomato genome ESTsd
Number of unigenes represented 15,373 30.8% 2911 52.9% 198 29.2% 9599
Number of unigenes with no match 34,618 69.2% 2593 47.1% 479 70.8% 17,675
Total unigenes 49,991 100.0% 5504 100.0% 667 100.0% 27,274
1 Metabolism 3173 16.8% 671 16.0% 102 27.3% 20.9%
2 Energy 1071 5.7% 295 7.1% 15 4.0% 4.0%
3 Cell growth, cell division, DNA synthesis 753 4.0% 199 4.8% 9 2.4% 2.8%
4 Transcription 1772 9.4% 381 9.1% 39 10.4% 11.3%
5 Protein synthesis 772 4.1% 286 6.8% 15 4.0% 4.1%
6 Protein destination 1268 6.7% 319 7.6% 26 7.0% 8.5%
7 Transport facilitation 1035 5.5% 185 4.4% 22 5.9% 5.9%
8 Cellular transport and transport mechanisms 851 4.5% 217 5.2% 14 3.7% 4.0%
9 Cellular biogenesis 1064 5.6% 193 4.6% 10 2.7% 2.7%
10 Cellular communication, signal transduction 2126 11.2% 359 8.6% 60 16.0% 13.6%
11 Cell rescue, defense, cell death, aging 1826 9.6% 334 8.0% 34 9.1% 8.0%
12 Ionic homeostasis 23 0.1% 2 0.0% 0 0.0% 0.0%
13 Cellular organization 2262 12.0% 588 14.1% 0 0.0% 13.7%
14 Motility 18 0.1% 2 0.0% 0 0.0% 0.0%
15 Tissue specificity 0 0.0% 0 0.0% 0 0.0% 0.0%
16 Development 639 3.4% 126 3.0% 4 1.1% 0.0%
17 Transposable elements, viral and plasmid 257 1.4% 25 0.6% 24 6.4% 0.0%
14 Organism-specific proteins 14 0.1% 0 0.0% 0 0.0% 0.0%
Number of matchese 18,924 100.0% 4182 100.0% 374 100.0% 99.5%
15 Classification not yet clear-cut 3603 666 54
16 Unclassified proteins 8112 1344 123
Total number of matches
30,639
6192
551

a The maize EST whole genome data (397,000 ESTs). Out of 49,991 unigenes (singletons and clusters), 15,373 (31%) could be assigned a putative function at 1e-10, which includes unclassified proteins and those whose classification is not yet clear-cut.

b Out of 5504 unigenes, 2911 (53%) could be assigned a putative function, which includes unclassified proteins and those whose classification is not yet clear-cut.

c Out of 5504 unigenes, 677 (12.3%) were not present in the maize EST collection of GenBank, of which only 198 had a match to MAt DB.

d Out of 27,274 unigenes, 9599 (35%) could be assigned a role category (Van der Hoeven et al. 2002).

e Number of matches exceeds the number of unigenes represented because the same unlgene may have more than one match from different role categories.