Supplementary Table 1: Transcriptomic analyses of E2FBOE plants. Genes differentially regulated at a stringency level of p<0.05. A) Up-regulated genes. B) down-regulated genes. C) Examples of the expression level of up-regulated selected genes in different organs and conditions using the digital expression data http://ted.bti.cornell.edu /cgibin/TFGD/array_data /home.cgi) are shown.

A complete data set has been sent to the National Centre for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) and can be found with the accession number GSE23971 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23971).

ProbeID / Fold Change / logSignal (A) / logRatio (M) / StdErr (logRatio) / Log
Control / StdErr
(logControl) / logExp / StdErr (logExp) / pval (LiMMA) / Description / E2F site / POSITION FROM ATG
1-1-1.4.10.11 / 8.29 / 12.68 / 3.05 / 0.25 / 11.15 / 0.27 / 14.20 / 0.45 / 0.00010211 / Ethylene-responsive proteinase inhibitor I precursor / YES / FIRST INTRON +251
1-1-5.1.1.11 / 7.78 / 12.78 / 2.96 / 0.16 / 11.30 / 0.11 / 14.26 / 0.26 / 0.00002974 / Ethylene-responsive proteinase inhibitor I precursor / YES / FIRST INTRON +252
1-1-5.4.13.11 / 6.04 / 11.16 / 2.59 / 0.22 / 9.86 / 0.53 / 12.46 / 0.34 / 0.00012821 / translation-inhibitor protein [Gentiana triflora] / YES / -150
1-1-1.1.14.12 / 5.57 / 10.36 / 2.48 / 0.19 / 9.12 / 0.16 / 11.60 / 0.30 / 0.00009655 / Wound-induced proteinase inhibitor II precursor / YES / -2500
1-1-5.1.13.2 / 5.48 / 10.14 / 2.45 / 0.20 / 8.91 / 0.38 / 11.36 / 0.39 / 0.00012774 / Wound-induced proteinase inhibitor II precursor / YES / -2000
1-1-3.3.13.17 / 5.12 / 10.56 / 2.36 / 0.06 / 9.39 / 0.49 / 11.74 / 0.47 / 0.00001541 / Wound-induced proteinase inhibitor II precursor / YES / -2000
1-1-7.4.10.15 / 4.55 / 10.05 / 2.18 / 0.13 / 8.96 / 0.43 / 11.15 / 0.54 / 0.00006467 / Wound-induced proteinase inhibitor II precursor / YES / -1650
1-1-3.4.10.13 / 4.17 / 12.49 / 2.06 / 0.17 / 11.46 / 0.26 / 13.52 / 0.43 / 0.00015571 / Wound-induced proteinase inhibitor I precursor / NO
1-1-8.4.13.20 / 4.06 / 9.24 / 2.02 / 0.22 / 8.23 / 0.70 / 10.25 / 0.49 / 0.00036186 / threonine deaminase / NO
1-1-4.3.16.11 / 3.94 / 9.63 / 1.98 / 0.04 / 8.64 / 0.47 / 10.62 / 0.50 / 0.00002521 / threonine deaminase / NO
1-1-5.4.10.14 / 3.85 / 12.04 / 1.95 / 0.29 / 11.06 / 0.18 / 13.01 / 0.39 / 0.00098402 / Wound-induced proteinase inhibitor I precursor / NO
1-1-3.3.13.20 / 3.37 / 9.87 / 1.75 / 0.17 / 8.99 / 0.59 / 10.74 / 0.41 / 0.00030580 / threonine deaminase / YES / -1000
1-1-3.2.13.15 / 3.35 / 9.87 / 1.74 / 0.09 / 9.00 / 0.46 / 10.74 / 0.40 / 0.00008483 / threonine deaminase / YES / -1000
1-1-3.4.9.3 / 3.27 / 9.84 / 1.71 / 0.03 / 8.98 / 0.53 / 10.69 / 0.50 / 0.00004291 / threonine deaminase / YES / -1000
1-1-1.2.10.8 / 3.18 / 12.35 / 1.67 / 0.26 / 11.52 / 0.07 / 13.19 / 0.21 / 0.00126378 / Wound-induced proteinase inhibitor I precursor / NO
1-1-6.1.16.4 / 2.77 / 8.80 / 1.47 / 0.60 / 8.06 / 0.99 / 9.53 / 1.59 / 0.02827165 / Wound-induced proteinase inhibitor II precursor / YES / -1200
1-1-6.3.14.12 / 2.73 / 12.18 / 1.45 / 0.11 / 11.46 / 0.39 / 12.91 / 0.35 / 0.00024082 / MADS box protein TDR3 - tomato (fragment) / NO
1-1-3.2.15.4 / 2.72 / 11.27 / 1.44 / 0.24 / 10.55 / 0.20 / 11.99 / 0.35 / 0.00168381 / Wound-induced proteinase inhibitor I precursor / YES / FIRST INTRON +300
1-1-1.2.1.13 / 2.72 / 14.97 / 1.44 / 0.51 / 14.25 / 0.31 / 15.69 / 0.21 / 0.01735163 / glutamate decarboxylase isozyme 1 [Nicotiana tabacum] / YES / -1700
1-1-2.3.1.20 / 2.71 / 12.10 / 1.44 / 0.11 / 11.38 / 0.34 / 12.82 / 0.41 / 0.00024758 / Wound-induced proteinase inhibitor I precursor / YES / 3´UTR
1-1-8.2.18.21 / 2.64 / 12.69 / 1.40 / 0.13 / 11.99 / 0.21 / 13.39 / 0.12 / 0.00036772 / Basic 30 kDa endochitinase precursor / NO
1-1-5.3.15.8 / 2.56 / 12.45 / 1.36 / 0.20 / 11.77 / 0.50 / 13.13 / 0.32 / 0.00124863 / Aminopeptidase 1, (Leucine aminopeptidase) / NO
1-1-3.4.8.19 / 2.53 / 10.09 / 1.34 / 0.22 / 9.42 / 0.34 / 10.75 / 0.54 / 0.00162539 / TDR4 transcription factor [Lycopersicon esculentum] / NO
1-1-3.1.18.12 / 2.53 / 9.60 / 1.34 / 0.08 / 8.93 / 0.76 / 10.27 / 0.68 / 0.00019069 / wound-induced protein Sn-1, vacuolar membrane - pepper / YES / -2000
1-1-8.2.17.4 / 2.52 / 12.18 / 1.33 / 0.20 / 11.51 / 0.29 / 12.85 / 0.26 / 0.00131448 / wound-induced protein (clone TAB7) - tomato (fragment) / YES / FIRST INTRON +420
1-1-8.2.16.10 / 2.47 / 12.28 / 1.31 / 0.25 / 11.62 / 0.27 / 12.93 / 0.25 / 0.00257921 / wound-induced protein (clone TAB7) - tomato (fragment) / YES / FIRST INTRON +421
1-1-2.2.7.11 / 2.45 / 14.71 / 1.29 / 0.44 / 14.06 / 0.33 / 15.35 / 0.11 / 0.01647147 / inorganic pyrophosphatase [Nicotiana tabacum] / NO
1-1-1.1.10.8 / 2.45 / 15.12 / 1.29 / 0.39 / 14.48 / 0.21 / 15.77 / 0.21 / 0.01107340 / glutamate decarboxylase isozyme 1 [Nicotiana tabacum] / YES / -1800
1-1-5.3.10.11 / 2.42 / 12.23 / 1.28 / 0.18 / 11.59 / 0.14 / 12.87 / 0.19 / 0.00123530 / wound-induced protein (clone TAB7) - tomato (fragment) / YES / INTRON + 4000
1-1-5.2.9.6 / 2.41 / 13.23 / 1.27 / 0.20 / 12.60 / 0.30 / 13.87 / 0.14 / 0.00151937 / Basic 30 kDa endochitinase precursor / NO
1-1-7.2.8.4 / 2.39 / 12.93 / 1.26 / 0.13 / 12.30 / 0.19 / 13.55 / 0.29 / 0.00054853 / Catalase isozyme 1 / YES / -500
1-1-4.3.6.6 / 2.39 / 14.65 / 1.26 / 0.17 / 14.02 / 0.33 / 15.28 / 0.17 / 0.00107557 / expressed protein [Arabidopsis thaliana] / YES / -3000
1-1-2.4.13.7 / 2.39 / 10.91 / 1.26 / 0.26 / 10.28 / 0.31 / 11.54 / 0.41 / 0.00327199 / Wound-induced proteinase inhibitor I precursor / NO
1-1-8.2.16.12 / 2.38 / 14.54 / 1.25 / 0.48 / 13.91 / 0.21 / 15.16 / 0.32 / 0.02292850 / glycerol-3-phosphate acyltransferase [Citrus unshiu] / NO
1-1-5.3.17.19 / 2.38 / 8.38 / 1.25 / 0.62 / 7.76 / 0.18 / 9.01 / 0.47 / 0.04858617 / putative DNA cytosine methyltransferase Zmet3 [Zea mays] / YES / -200
1-1-4.1.6.3 / 2.35 / 10.74 / 1.23 / 0.06 / 10.12 / 0.17 / 11.35 / 0.18 / 0.00020875 / OSJNBa0027P08.6 [Oryza sativa (japonica cultivar-group)] / YES / -500
1-1-6.3.1.19 / 2.34 / 11.72 / 1.22 / 0.17 / 11.11 / 0.16 / 12.33 / 0.18 / 0.00109558 / OSMOTIN-LIKE PROTEIN OSML15 PRECURSOR (PA15) / YES / -500
1-1-2.3.10.15 / 2.34 / 12.81 / 1.23 / 0.30 / 12.20 / 0.17 / 13.43 / 0.31 / 0.00578027 / pathogenesis-related protein PR-1 precursor / YES / -2500
1-1-1.2.12.21 / 2.32 / 12.50 / 1.21 / 0.28 / 11.90 / 0.06 / 13.11 / 0.27 / 0.00478953 / pathogenesis-related protein PR-1 precursor / YES / -2500
1-1-1.2.9.4 / 2.29 / 9.11 / 1.20 / 0.20 / 8.51 / 0.40 / 9.71 / 0.39 / 0.00206776 / Acidic 26 kDa endochitinase precursor / YES / -70
1-1-8.2.14.16 / 2.27 / 11.76 / 1.18 / 0.20 / 11.16 / 0.19 / 12.35 / 0.26 / 0.00191079 / CER1 protein [Arabidopsis thaliana] / NO
1-1-5.1.2.6 / 2.25 / 11.52 / 1.17 / 0.10 / 10.93 / 0.05 / 12.10 / 0.14 / 0.00046468 / expressed protein [Arabidopsis thaliana] / NO
1-1-3.3.20.15 / 2.25 / 14.25 / 1.17 / 0.30 / 13.66 / 0.20 / 14.83 / 0.21 / 0.00692638 / copine BONZAI1 (BON1) [Arabidopsis thaliana] / NO
1-1-5.2.6.4 / 2.24 / 14.22 / 1.17 / 0.17 / 13.64 / 0.30 / 14.81 / 0.15 / 0.00145698 / RelA-SpoT like protein RSH1 [Nicotiana tabacum] / NO
1-1-6.3.9.6 / 2.23 / 14.56 / 1.16 / 0.18 / 13.98 / 0.23 / 15.14 / 0.05 / 0.00171384 / putative chloroplast thiazole biosynthetic protein / NO
1-1-5.1.3.19 / 2.21 / 13.47 / 1.14 / 0.33 / 12.90 / 0.17 / 14.04 / 0.22 / 0.01060374 / GH3 protein -related [Arabidopsis thaliana] / YES / -2000
1-1-5.4.12.8 / 2.19 / 10.94 / 1.13 / 0.29 / 10.37 / 0.07 / 11.50 / 0.22 / 0.00719686 / Polygalacturonase 2A precursor (PG-2A) (Pectinase) / NO
1-1-3.3.13.3 / 2.19 / 13.49 / 1.13 / 0.20 / 12.92 / 0.33 / 14.05 / 0.13 / 0.00255987 / Aspartic protease inhibitor 1 precursor (pA1) / YES / -3000
1-1-1.3.18.1 / 2.19 / 11.76 / 1.13 / 0.05 / 11.20 / 0.07 / 12.33 / 0.12 / 0.00027404 / OSJNBa0093F12.21 [Oryza sativa (japonica cultivar-group)] / YES / -500
1-1-7.1.3.11 / 2.18 / 11.47 / 1.12 / 0.07 / 10.91 / 0.09 / 12.03 / 0.10 / 0.00033337 / ethylene response factor 3 [Lycopersicon esculentum] / YES / -50
1-1-5.3.7.10 / 2.18 / 11.60 / 1.12 / 0.06 / 11.03 / 0.36 / 12.16 / 0.32 / 0.00031458 / bacterial IS-element [Arabidopsis thaliana] / NO
1-1-1.4.15.16 / 2.17 / 8.74 / 1.12 / 0.54 / 8.19 / 0.05 / 9.30 / 0.59 / 0.04614612 / probable bHLH transcription factor / YES / 3´UTR
1-1-8.3.7.20 / 2.16 / 10.12 / 1.11 / 0.10 / 9.57 / 0.17 / 10.67 / 0.07 / 0.00056309 / putative DNA-binding protein [Arabidopsis thaliana] / NO
1-1-5.2.9.1 / 2.16 / 15.25 / 1.11 / 0.25 / 14.70 / 0.17 / 15.81 / 0.18 / 0.00513404 / potential chimera / n/d
1-1-8.4.14.7 / 2.14 / 9.70 / 1.10 / 0.44 / 9.15 / 0.24 / 10.25 / 0.44 / 0.02846077 / Peptidyl-prolyl cis-trans isomerase (Cyclosporin A-binding ) / NO
1-1-7.4.12.13 / 2.13 / 12.88 / 1.09 / 0.22 / 12.33 / 0.15 / 13.42 / 0.28 / 0.00351697 / pathogenesis-related protein PR-1 precursor / YES / -2600
1-1-3.2.14.6 / 2.13 / 11.55 / 1.09 / 0.51 / 11.01 / 0.43 / 12.10 / 0.19 / 0.04286912 / quinone reductase family [Arabidopsis thaliana] / YES / -1400
1-1-6.3.9.8 / 2.12 / 12.79 / 1.08 / 0.07 / 12.25 / 0.14 / 13.33 / 0.14 / 0.00039748 / extensin homolog - potato (fragment) / NO
1-1-2.2.7.5 / 2.07 / 11.95 / 1.05 / 0.46 / 11.42 / 0.45 / 12.47 / 0.04 / 0.03681932 / ELONGATION FACTOR G, CHLOROPLAST PRECURSOR (EF-G) / NO
1-1-1.2.2.13 / 2.07 / 9.28 / 1.05 / 0.13 / 8.75 / 0.26 / 9.80 / 0.36 / 0.00103977 / Acidic 26 kDa endochitinase precursor / YES / - 70
1-1-6.3.14.8 / 2.06 / 8.88 / 1.04 / 0.21 / 8.36 / 0.11 / 9.40 / 0.22 / 0.00372386 / Acidic 26 kDa endochitinase precursor / YES / - 50
1-1-7.4.7.10 / 2.04 / 11.94 / 1.03 / 0.10 / 11.43 / 0.19 / 12.45 / 0.22 / 0.00075968 / putative alcohol dehydrogenase [Lycopersicon esculentum] / NO
1-1-7.4.12.12 / 2.04 / 11.08 / 1.03 / 0.31 / 10.57 / 0.10 / 11.59 / 0.30 / 0.01258486 / Polygalacturonase 2A precursor (PG-2A) (Pectinase) / NO
1-1-1.3.2.20 / 2.04 / 12.51 / 1.03 / 0.25 / 12.00 / 0.14 / 13.03 / 0.20 / 0.00636749 / wound-induced protein Sn-1, vacuolar membrane - pepper / NO
1-1-4.2.13.3 / 2.03 / 9.69 / 1.02 / 0.11 / 9.18 / 0.18 / 10.20 / 0.16 / 0.00096051 / thioredoxin family [Arabidopsis thaliana] / NO
ProbeID / Fold Change / logSignal (A) / logRatio (M) / StdErr (logRatio) / logControl / StdErr (logControl) / logExp / StdErr (logExp) / pval (LiMMA) / Description / E2F site / Position from ATG
1-1-5.1.10.14 / -2.35 / 10.73 / -1.24 / 0.09 / 11.35 / 0.20 / 10.11 / 0.29 / 0.00034439 / putative early light induced protein [Arachis hypogaea] / NO
1-1-6.3.1.12 / -2.28 / 11.07 / -1.19 / 0.07 / 11.66 / 0.19 / 10.47 / 0.15 / 0.00029728 / aminotransferase 1 [Cucumis melo] / NO
1-1-3.2.6.2 / -2.24 / 7.19 / -1.16 / 0.43 / 7.77 / 0.07 / 6.61 / 0.50 / 0.02135234 / Uroporphyrinogen decarboxylase, chloroplast precursor (URO-D) (UPD) / NO
1-1-1.1.4.14 / -2.22 / 12.91 / -1.15 / 0.29 / 13.49 / 0.32 / 12.34 / 0.58 / 0.00671889 / Ribulose bisphosphate carboxylase/oxygenase activase 1, (RuBisCO activase 1) / NO
1-1-6.2.2.11 / -2.22 / 7.89 / -1.15 / 0.46 / 8.46 / 0.14 / 7.31 / 0.59 / 0.02701459 / putative zinc finger protein [Arabidopsis thaliana] / NO
1-1-8.4.19.2 / -2.17 / 9.18 / -1.12 / 0.10 / 9.74 / 0.22 / 8.62 / 0.30 / 0.00059710 / putative acyl-CoA synthetase [Capsicum annuum] / YES / INTRON +700
1-1-1.2.9.3 / -2.16 / 9.92 / -1.11 / 0.21 / 10.47 / 0.28 / 9.36 / 0.32 / 0.00301570 / chloroplast 30S ribosomal protein S31 [Arabidopsis thaliana] / NO
1-1-1.3.9.8 / -2.15 / 12.97 / -1.10 / 0.23 / 13.53 / 0.13 / 12.42 / 0.31 / 0.00384675 / expressed protein [Arabidopsis thaliana] / no
1-1-2.2.2.8 / -2.14 / 14.35 / -1.10 / 0.10 / 14.90 / 0.34 / 13.80 / 0.25 / 0.00057416 / Ribulose bisphosphate carboxylase/oxygenase activase (RuBisCO activase) / NO
1-1-2.2.10.9 / -2.14 / 10.42 / -1.10 / 0.18 / 10.97 / 0.21 / 9.87 / 0.35 / 0.00193504 / FRUCTOSE-1,6-BISPHOSPHATASE, CYTOSOLIC (CY-F1) / YES / -3200
1-1-2.2.14.9 / -2.13 / 7.53 / -1.09 / 0.24 / 8.07 / 0.15 / 6.98 / 0.34 / 0.00475897 / unknown protein [Oryza sativa (japonica cultivar-group)] / NO
1-1-5.2.12.11 / -2.11 / 9.03 / -1.08 / 0.05 / 9.57 / 0.17 / 8.49 / 0.22 / 0.00030910 / Phytoene synthase 1, chloroplast precursor (Fruit ripening specific protein pTOM5) / NO
1-1-1.1.13.19 / -2.09 / 10.08 / -1.06 / 0.25 / 10.61 / 0.29 / 9.55 / 0.23 / 0.00581484 / CIG1 [Nicotiana tabacum] / YES / -700
1-1-4.1.1.10 / -2.09 / 14.26 / -1.06 / 0.05 / 14.79 / 0.18 / 13.73 / 0.23 / 0.00034212 / Ribulose bisphosphate carboxylase/oxygenase activase(RuBisCO activase) / NO
1-1-2.2.1.11 / -2.08 / 12.29 / -1.06 / 0.08 / 12.82 / 0.42 / 11.76 / 0.34 / 0.00052023 / Putative Glucan 1,3-beta-glucosidase precursor / NO
1-1-6.2.6.14 / -2.07 / 9.04 / -1.05 / 0.08 / 9.56 / 0.21 / 8.51 / 0.21 / 0.00049804 / remorin 1 [Lycopersicon esculentum] / NO
1-1-3.3.19.8 / -2.04 / 8.20 / -1.03 / 0.38 / 8.72 / 0.23 / 7.69 / 0.17 / 0.02234425 / expressed protein [Arabidopsis thaliana] / NO
1-1-6.4.19.19 / -2.01 / 11.63 / -1.01 / 0.08 / 12.13 / 0.15 / 11.12 / 0.08 / 0.00056719 / Glyceraldehyde 3-phosphate dehydrogenase B / NO