Table 7

KOG-assigned EST clusters predicted to be highly 2N-specific based on statistical comparison of libraries

Cluster ID

Number of 2N ESTs

P-value

Homolog ID

Homolog description

BLAST


Carbohydrate transport and metabolism

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


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.

von Dassow et al. Genome Biology 2009 10:R114   doi:10.1186/gb-2009-10-10-r114

Open Data