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
|
|
|
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↵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.
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↵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.
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↵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.
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↵d Out of 27,274 unigenes, 9599 (35%) could be assigned a role category (Van der Hoeven et al. 2002).
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↵e Number of matches exceeds the number of unigenes represented because the same unlgene may have more than one match from different role categories.
