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Table 3 In silicoscreening and transcriptional analysis by real-time RT-PCR.

From: Characterization of expressed sequence tags obtained by SSH during somatic embryogenesis in Cichorium intybus L

   

In silico analyses

real-time RT-PCR

Acc. nb

Contig/OC

Putative function

E

NE

P

Pred

p-value

ER 1

ER 2

DT212490

Cont0080

vegetative storage protein, VSP [C. intybus]

5

0

]0.08;0.07[

E

   

DT212771

Cont4942

elongation factor EF-2 [P. sativum]

10

0

]0.006;0.005[

E

0.09435

-0.18

0.38

DT212374

Cont9008

Shaggy-like kinase tetha [A. thaliana]

5

0

]0.08;0.07[

E

   

DT212650

OC0603_a

methionine synthase [S. tuberosum]

6

0

]0.05;0.04[

E

   

DT212300

OC1814

No hits found

5

0

]0.08;0.07[

E

<0.000001*

2.00*

1.90*

DT212502

OC1929

G protein beta subunit [N. plumbaginifolia]

5

0

]0.08;0.07[

E

<0.000001*

1.25*

1.24*

DT213897

Cont0011

catalase 3 [H. annuus]

4

8

]0.09;0.08[

NE

<0.000001*

-3.85*

-3.88*

DT211305

Cont0015

L-asparaginase [G. max]

0

3

]0.07;0.06[

NE

0.03694

0.18

0.40

DT211671

Cont0026

ss-1,3-glucanase [C. intybus × C. endivia]

0

3

]0.07;0.06[

NE

<0.000001*

-2.87*

-4.10*

DT213305

Cont0060

3-hydroxy-3-methylglutaryl coenzyme A reductase [S. tuberosum]

8

15

]0.03;0.02[

NE

<0.000001*

-2.30*

-2.03*

DT212144

Cont0082

putative argininosuccinate synthase [A. thaliana]

0

4

]0.03;0.02[

NE

0.00095*

1.23*

0.70*

DT210848

Cont0112

heat shock protein 70 like protein [A. thaliana]

0

3

]0.07;0.06[

NE

   

DT211362

Cont0201

putative auxin-induced protein [A. thaliana]

0

5

]0.02;0.01[

NE

<0.000001*

-1.88*

-2.03*

DT211152

Cont0206

fasciclin-like AGP 12 [P. alba × P. tremula]

0

4

]0.03;0.02[

NE

0.00538

-0.25

-0.40

DT211657

Cont1237

pre-pro-cysteine proteinase [L. esculentum]

0

4

]0.03;0.02[

NE

<0.000001*

-2.32*

-3.00*

DT211016

Cont1242

unknown protein [A. thaliana]

0

3

]0.07;0.06[

NE

   

DT210870

Cont9022

unknown yeast pheromone receptor-like protein AR781 [A. thaliana]

0

3

]0.07;0.06[

NE

   

DT213289

Cont9039

metallothionein 1 [A. tripolium]

14

26

]0.004;0.003[

NE

<0.000001*

-2.45*

-2.45*

DT210772

OC0003_b

glutathione S-transferase GST 13 [G. max]

0

4

]0.03;0.02[

NE

   

DT212623

OC0023_a

glutathione transferase [H. muticus]

3

11

]0.007;0.006[

NE

<0.000001*

-2.78*

-2.85*

DT211055

OC0168

1-aminocyclopropane-1-carboxylate oxidase [L. esculentum]

0

9

<0.001

NE

<0.000001*

-3.87*

-3.80*

DT210897

OC0178

putative ribosomal S29 protein [A. thaliana]

0

3

]0.07;0.06[

NE

<0.000001*

1.15*

0.70*

DT210805

OC0344

unknown protein [A. thaliana]

0

3

]0.07;0.06[

NE

<0.000001*

-1.35*

-1.68*

DT211689

OC0378_b

putative 60S ribosomal protein L5 [O. sativa]

0

3

]0.07;0.06[

NE

   

DT214125

OC0533b

lipid transfer protein precursor [M. domestica]

2

7

]0.04;0.03[

NE

0.06214

-0.18

-0.25

DT211562

OC0559

putative phosphatase type 2C [A. thaliana]

0

3

]0.07;0.06[

NE

0.01554

-0.25

-0.25

DT211372

OC0631

No hits found

0

3

]0.07;0.06[

NE

0.03982

0.20

0.20

DT211599

OC0686

unknown protein [A. thaliana]

0

4

]0.03;0.02[

NE

<0.000001*

-3.37*

-3.23*

DT211633

OC0696

aquaporin [H. annuus]

0

3

]0.07;0.06[

NE

<0.000001*

-3.72*

-3.52*

DT211922

OC0724

cellulose synthase family protein [A. thaliana]

0

3

]0.07;0.06[

NE

<0.000001*

-2.60*

-2.47*

DT211365

OC0727_b

G protein beta subunit-like [M. sativa]

0

5

]0.02;0.01[

NE

   

DT210839

OC0758

putative RNA-binding protein [A. thaliana]

0

5

]0.02;0.01[

NE

0.01647

0.08

0.18

DT212897

OC1229

sucrose synthase isoform I [D. carota]

1

5

]0.05;0.04[

NE

0.30612

0.08

-0.32

DT212813

OC0311_a

acidic ribosomal protein P0 [G. max]

6

2

  

<0.000001*

1.62*

1.68*

DT212479

OC0378_c

60S ribosomal protein L5 [C. sativus]

1

3

  

<0.000001*

0.58*

0.85*

DT211177

OC0805_a

putative 60S ribosomal protein L35 [A. thaliana]

0

1

  

0.00001*

1.10*

0.73*

DT212655

OC1088

ribosomal protein L12 [C. intybus]

1

1

  

0.00013*

1.25*

0.95*

DT213187

OC1549_a

40S ribosomal protein S17 [L. esculentum]

2

1

  

<0.000001*

1.72*

1.55*

DT212250

OC2155_a

P40-like ribosomal protein [D. carota]

3

0

  

0.00003*

0.58*

0.82*

DT212554

Cont0001

glyceraldehyde-3-phosphate dehydrogenase [S. alba]

9

2

  

<0.000001*

1.20*

0.97*

DT210799

Cont0006

1-aminocyclopropane-1-carboxylate oxidase [P. hortorum]

2

5

  

<0.000001*

-3.82*

-4.28*

DT211255

Cont0024

seed specific protein Bn15D17A [B. napus]

3

5

  

0.25124

0.00

0.13

DT211067

Cont6402

putative leaf development protein Argonaute [A. thaliana]

1

1

  

<0.000001*

1.37*

1.37*

DT210888

OC0071

14-3-3 protein [S. tuberosum]

0

1

  

<0.000001*

-1.78*

-2.05*

DT210862

OC0172

embryogenic callus protein 181 [D. carota]

0

2

  

0.56355

-0.28

0.05

DT211413

OC0565_a

acetoacetyl-CoA thiolase [A. thaliana]

0

2

  

<0.000001*

-2.52*

-2.42*

DT212452

OC0603_b

cobalamine-independent methionine synthase [S. scutellarioides]

7

1

  

<0.000001*

-1.90*

-1.57*

DT212234

OC0687

arabinogalactan protein [D. carota]

7

1

  

<0.000001*

6.73*

6.82*

DT212237

OC0834

chromatin remodeling factor CHD3 [A. thaliana]

1

0

  

0.00042

0.50

0.50

DT212556

OC1068

leaf senescence protein-related (YLS7) [A. thaliana]

2

0

  

<0.000001*

-1.55*

-1.38*

DT212596

OC1155

xyloglucan endotransglycosylase [M. domestica]

2

0

  

0.00011

-0.57

-0.52

DT212803

OC1211

BTB/POZ domain-containing protein [A. thaliana]

2

0

  

0.00365

0.38

0.42

DT213079

OC1347

putative ethylene response element binding protein [N. tabacum]

1

2

  

0.00007*

-1.45*

-1.22*

DT212789

OC1427_b

Cell division control protein 48 homolog E [A. thaliana]

2

0

  

0.00001*

0.60*

0.60*

DT213276

OC1785_a

H(+)-transporting ATPase [P. vulgaris]

2

0

  

0.00002*

-0.87*

-0.93*

DT212233

OC1796

ring domain containing protein [C. annuum]

10

8

  

<0.000001*

-2.18*

-2.35*

DT212829

OC1960

tuber-specific/sucrose-responsive element binding factor [S. tuberosum]

4

0

  

0.00021

-0.15

-0.65

  1. Contig/OC: contig or OC (Original Cluster regrouping identical ESTs) number. Putative functions were determined by a BlastX search (E-value ≤ E-5) against the non redundant GenBank database. E and NE: number of ESTs from the E and the NE library, respectively; p: probability related to the in silico prediction calculated according to Audic and Claverie [25]. Pred (prediction) indicates in which genotype (E or NE) the gene was found preferentially expressed. ER: expression ratios (log2) between the embryogenic and the non-embryogenic genotype at day 4 of SE culture estimated by real-time RT-PCR. ER1 and ER2 designate the expression ratios obtained from 2 independent first strand cDNA synthesis reactions (see Methods). The asterisk indicates genes that were found to be differentially expressed according the thresholds applied (see Methods).
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BMC Plant Biology

ISSN: 1471-2229

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