Table 7 |
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|
KOG-assigned EST clusters predicted to be highly 2N-specific based on statistical comparison of libraries |
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|
Cluster ID |
Number of 2N ESTs |
P-value |
Homolog ID |
Homolog description |
BLAST |
|
|
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|
Carbohydrate transport and metabolism |
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|
GS00451 |
7 |
3.9 × 10-3 |
PIP25_ARATH |
Probable aquaporin PIP2-5 |
1 × 10-34 |
|
GS00433 |
8 |
1.9 × 10-3 |
F26_RANCA |
6PF-2-K/Fru-2,6-P2ASE liver/muscle isozymes |
3 × 10-40 |
|
Cell wall/membrane/envelope biogenesis |
|||||
|
GS01290 |
8 |
1.9 × 10-3 |
ASB3_BOVIN |
Ankyrin repeat and SOCS box protein 3 (ASB-3) |
9 × 10-06 |
|
Chromatin structure and dynamics |
|||||
|
GS02435 |
6 |
7.8 × 10-3 |
H4_OLILU |
Histone H4 |
8 × 10-33 |
|
Cytoskeleton |
|||||
|
GS00171 |
6 |
7.8 × 10-3 |
EXS_ARATH |
Leucine-rich repeat receptor protein kinase EXS precursor |
1 × 10-08 |
|
Energy production and conversion |
|||||
|
GS00763 |
6 |
7.8 × 10-3 |
QORH_ARATH |
Putative chloroplastic quinone-oxidoreductase homolog |
6 × 10-25 |
|
GS01632 |
7 |
3.9 × 10-3 |
CYPD_BACSU |
Probable bifunctional P-450/NADPH-P450 reductase 1 |
2 × 10-43 |
|
General function prediction only |
|||||
|
GS00580 |
9 |
9.7 × 10-4 |
YMO3_ERWST |
Uncharacterized protein in mobD 3' region |
6 × 10-07 |
|
GS02524 |
7 |
3.9 × 10-3 |
†RKIP |
Raf kinase inhibitor protein (RKIP), Phosphatidylethanolamine-binding protein (PEBP) |
1 × 10-06 |
|
Inorganic ion transport and metabolism |
|||||
|
GS00463 |
8 |
1.9 × 10-3 |
NCKXH_DROME |
Probable Na+/K+/Ca2+ exchanger CG1090 |
1 × 10-22 |
|
GS05051 |
7 |
3.9 × 10-3 |
B3A2_RAT |
Anion exchange protein 2 (AE2 anion exchanger) |
8 × 10-14 |
|
Intracellular trafficking, secretion, and vesicular transport |
|||||
|
GS02941 |
9 |
9.7 × 10-4 |
STX1A_CAEEL |
Syntaxin-1A homolog |
2 × 10-19 |
|
Lipid transport and metabolism |
|||||
|
GS00955 |
7 |
3.9 × 10-3 |
S5A1_MACFA |
3-oxo-5-alpha-steroid 4-dehydrogenase 1 |
3 × 10-54 |
|
Posttranslational modification, protein turnover, chaperones |
|||||
|
GS06447 |
6 |
7.8 × 10-3 |
CLPP3_ANASP |
Probable ATP-dependent Clp protease proteolytic subunit 3 |
2 × 10-31 |
|
GS02029 |
8 |
1.9 × 10-3 |
UBCY_ARATH |
Ubiquitin-conjugating enzyme E2-18 kDa |
4 × 10-20 |
|
GS03925 |
8 |
1.9 × 10-3 |
FKBP4_DICDI |
FK506-binding protein 4 (peptidyl-prolyl cis-trans isomerase) |
1 × 10-07 |
|
Replication, recombination and repair |
|||||
|
GS00109 |
8 |
1.9 × 10-3 |
MCM2_XENTR |
DNA replication licensing factor mcm2 |
1 × 10-109 |
|
Secondary metabolites biosynthesis, transport and catabolism |
|||||
|
GS00417 |
6 |
7.8 × 10-3 |
WBC11_ARATH |
White-brown complex homolog protein 11 |
9 × 10-28 |
|
Signal transduction mechanisms |
|||||
|
GS00826 |
6 |
7.8 × 10-3 |
STK4_BOVIN |
Serine/threonine-protein kinase 4 |
2 × 10-47 |
|
GS00712 |
7 |
3.9 × 10-3 |
PI4K_DICDI |
Phosphatidylinositol 4-kinase |
3 × 10-43 |
|
GS00083 |
7 |
3.9 × 10-3 |
SHKE_DICDI |
Dual specificity protein kinase shkE |
9 × 10-22 |
|
GS01230 |
7 |
3.9 × 10-3 |
†PP2Cc |
Serine/threonine phosphatases, family 2C, catalytic domain |
2 × 10-08 |
|
|
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|
Only clusters with zero ESTs originating from the 1N library are shown. The number of 2N EST reads in each cluster and the P-value for significance of the difference between libraries are shown. Homolog IDs are marked as in Table 5. Clusters are arranged by KOG class. Clusters in bold were chosen for RT-PCR validation. Additional data file 5 gives a complete list of all clusters predicted to be 2N-specific by statistical comparison of libraries. |
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|
von Dassow et al. Genome Biology 2009 10:R114 doi:10.1186/gb-2009-10-10-r114 |
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