Functional classification of the gerbera EST collection
|
|
Total |
Late petal |
Infloresc |
Botrytis infected |
Stamen |
Leaf |
Scape |
Early petal |
Regina pappus |
Nero pappus |
|---|---|---|---|---|---|---|---|---|---|---|
| ESTs | 16994 | 2442 | 3726 | 1919 | 1818 | 1620 | 1643 | 1169 | 1511 | 1146 |
| UniGenes | 8098 | 1335 | 2190 | 1202 | 1350 | 1160 | 1249 | 947 | 1109 | 614 |
| Clusters | 2591 | 258 | 357 | 390 | 225 | 244 | 232 | 132 | 196 | 237 |
| Singletons | 5507 | 1077 | 1833 | 812 | 1125 | 916 | 1017 | 815 | 913 | 377 |
| Clusters (%) | 32.0 | 19.3 | 16.3 | 32.5 | 16.7 | 21.0 | 18.6 | 14.9 | 17.7 | 38.6 |
| Singletons (%)
|
68.0
|
80.7
|
83.7
|
67.6
|
83.3
|
79.0
|
81.4
|
86.1
|
82.3
|
61.4
|
| %
|
%
|
%
|
%
|
%
|
%
|
%
|
%
|
%
|
%
|
|
|---|---|---|---|---|---|---|---|---|---|---|
| a) Match Arabidopsis Funcat (1e-10) | 41.5 | 50.5 | 44.5 | 32.9 | 46.3 | 52.5 | 35.0 | 57.9 | 31.7 | 21.0 |
| b) Ambiguous/unknown function | 12.4 | 14.0 | 12.0 | 8.3 | 12.8 | 12.3 | 7.5 | 15.0 | 7.5 | 5.9 |
| c) Functionally annotated | 29.2 | 36.5 | 32.5 | 24.5 | 33.5 | 40.2 | 27.5 | 42.9 | 24.3 | 15.1 |
| d) [01] Metabolism | 9.2 | 11.8 | 8.0 | 8.3 | 11.6 | 13.1 | 9.6 | 11.8 | 7.9 | 6.0 |
| [02] Energy | 3.7 | 4.1 | 3.5 | 2.7 | 4.7 | 8.8 | 4.1 | 4.5 | 1.8 | 2.8 |
| [03] Cell growth | 1.9 | 2.8 | 2.6 | 1.5 | 2.8 | 2.0 | 1.3 | 1.9 | 1.3 | 1.0 |
| [04] Transcription | 4.6 | 5.8 | 6.4 | 2.3 | 4.5 | 4.2 | 3.0 | 7.0 | 3.1 | 1.3 |
| [05] Protein synthesis | 2.7 | 4.9 | 4.2 | 2.5 | 3.0 | 5.3 | 3.5 | 7.6 | 2.3 | 1.0 |
| [06] Protein destination | 3.7 | 5.4 | 3.8 | 3.2 | 3.9 | 4.7 | 3.4 | 5.6 | 3.2 | 1.8 |
| [07] Transport facilitation | 2.7 | 2.8 | 2.6 | 2.7 | 4.1 | 2.8 | 2.6 | 3.5 | 2.9 | 1.6 |
| [08] Cellular transport & transport mechanisms | 2.3 | 3.2 | 2.5 | 3.2 | 3.6 | 2.4 | 2.6 | 3.3 | 2.1 | 2.0 |
| [09] Cellular biogenesis | 3.0 | 4.0 | 3.3 | 2.7 | 4.1 | 3.4 | 3.9 | 4.0 | 3.1 | 2.0 |
| [10] Cellular communication/signal transduction | 4.7 | 4.8 | 5.2 | 3.5 | 5.9 | 4.7 | 3.6 | 5.6 | 4.0 | 1.5 |
| [11] Cell defense | 4.7 | 6.9 | 4.8 | 3.7 | 6.4 | 7.0 | 4.3 | 6.4 | 4.5 | 1.5 |
| [13] Ionic homeostasis | 0.1 | 0.2 | 0.1 | 0.3 | 0.1 | 0.3 | 0.2 | 0.3 | 0.3 | 0.2 |
| [30] Cellular organisation | 7.3 | 10.4 | 10.3 | 5.2 | 8.0 | 12.1 | 6.7 | 13.0 | 5.1 | 3.7 |
| [35] Motility | 0.0 | 0.1 | 0.0 | 0.0 | 0.0 | 0.2 | 0.1 | 0.0 | 0.0 | 0.0 |
| [50] Development | 1.6 | 1.9 | 1.7 | 1.5 | 1.7 | 1.9 | 1.1 | 1.7 | 0.8 | 0.2 |
| [90] Transposable elements | 0.3 | 0.0 | 0.4 | 0.2 | 0.3 | 0.3 | 0.1 | 0.3 | 0.1 | 0.0 |
| [97] Organism specific proteins | 0.1 | 0.1 | 0.0 | 0.0 | 0.1 | 0.0 | 0.1 | 0.0 | 0.0 | 0.0 |
| e) No match to Arabidopsis Funcat | 58.5 | 49.5 | 55.5 | 67.1 | 53.7 | 47.5 | 65.0 | 42.1 | 68.3 | 79.0 |
| f) Short peptides (discarded) | 13.7 | 7.3 | 9.9 | 23.5 | 11.9 | 9.0 | 21.1 | 5.8 | 22.2 | 40.6 |
| g) Novel gerbera CDS
|
44.8
|
42.2
|
45.6
|
43.6
|
41.8
|
38.5
|
43.9
|
36.3
|
46.1
|
38.4
|
-
BLASTX was performed against functionally annotated Arabidopsis proteins (MIPS Funcat) and the results were filtered using the expectation value of 1e-10. This results in UniGenes that correspond to a functionally annotated protein (a) and a population of apparently novel UniGenes (e). The functionally annotated class represents proteins of known function, but also includes sequences of 27 unknown or unclear function (MIPS Funcat codes 98 and 99). Sequences that cannot be assigned to a functional class (b) are described separately from the sequences that can be assigned a putative function (c). The distribution of distinct functional classes is summarized in (d). Note that a typical peptide is assigned more than one function so the sum of assignments is greater than the whole. The sequences that show no clear homolog to a functionally annotated Arabidopsis protein have been further separated into the sequences that have a short peptide (f) and the sequences that have a long peptide and represent putative Gerbera specific CDS. All sequences may be summed by (b) + (c) + (f) + (g).
