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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).