Table 1.
Immediate transcriptional targets of ARR
| Locus | non-transgenic untreated mean | non-transgenic β-est treated mean | FC non-transgenic | Adjusted FC non-transgenic | ARR2-ER transgenic untreated mean | ARR2-ER transgenic β-est treated mean | FC ARR2-ER transgenic | pvalue | qvalue | transgenic adjusted FC-nontransgenic | Gene description |
| At1g74890 | 197.5 | 185.4 | 0.94 | 1.00 | 102.5 | 1802.4 | 17.58 | 1.47E-04 | 6.91E-02 | 17.58 | ARR15 |
| At1g34330 | 5.7 | 2 | 0.35 | 1.00 | 1.4 | 23.7 | 16.63 | 3.49E-03 | 1.30E-01 | 16.63 | putative peroxidase |
| At1g10460 | 19.8 | 18.1 | 0.91 | 1.00 | 4.5 | 49.5 | 10.89 | 3.49E-03 | 1.30E-01 | 10.89 | germ in-like protein |
| At2g14270 | 11.2 | 1.9 | 0.17 | 1.00 | 1.8 | 16.7 | 9.10 | 2.30E-03 | 1.17E-01 | 9.10 | putative protein phosphatase 2C |
| At5g62920 | 300.1 | 310.1 | 1.03 | 1.03 | 228.5 | 1906.3 | 8.34 | 4.04E-04 | 7.96E-02 | 8.07 | ARR6 |
| At3g28890 | 23.4 | 5.4 | 0.23 | 1.00 | 2.8 | 19.6 | 6.90 | 5.80E-03 | 1.50E-01 | 6.90 | leucine-rich repeat family protein |
| At4g19770 | 28 | 339 | 1.21 | 1.21 | 2.4 | 19.2 | 7.99 | 1.11E-03 | 105E-C1 | 6.59 | glycosyl hydrolase family 18 protein |
| At5g45830 | 56.6 | 33.9 | 0.60 | 1.00 | 12 | 78.1 | 6.54 | 3.03E-03 | 1.23E-01 | 6.54 | expressed protein |
| At1g04840 | 42.1 | 28 | 0.66 | 1.00 | 5.5 | 36 | 6.49 | 7.49E-06 | 3.82E-02 | 6.49 | pentatricopeptide (PPR) repeat protein |
| At5g45650 | 215.1 | 194.1 | 0.90 | 1.00 | 402.7 | 2536 | 6.30 | 2.76E-07 | 2.33E-03 | 6.30 | subtilisin-like protease |
| At2g40670 | 378.2 | 338.6 | 0.90 | 1.00 | 516.4 | 3072.7 | 5.95 | 3.38E-05 | 5.89E-02 | 5.95 | ARR16 |
| At5g56970 | 146.3 | 192.7 | 1.32 | 1.32 | 159.2 | 1217.2 | 7.64 | 5.83E-03 | 1.50E-01 | 5.80 | cytokinin oxidase family protein |
| At1g10470 | 1715.8 | 1511.8 | 0.88 | 1.00 | 1150 | 6186.8 | 5.38 | 3.13E-04 | 7.33E-02 | 5.38 | ARR4 |
| At1g16530 | 98.7 | 137.8 | 1.40 | 1.40 | 138.8 | 1033.8 | 7.45 | 9.55E-04 | 1.02E-01 | 5.33 | lateral organ boundaries protein 3 |
| At3g48100 | 1219.9 | 1554.9 | 1.27 | 1.27 | 1043.5 | 6345.8 | 6.08 | 5.40E-03 | 1.47E-01 | 4.77 | ARR5 |
| At3g57040 | 681.3 | 581.6 | 0.85 | 1.00 | 490.4 | 2284 | 4.66 | 1.70E-04 | 6.91E-02 | 4.66 | ARR9 |
| At2g01890 | 412.5 | 243.1 | 0.59 | 1.00 | 432.2 | 1938.8 | 4.49 | 8.31E-08 | 1.40E-03 | 4.49 | putative purple acid phosphatase |
| At4g26010 | 63.1 | 53.8 | 0.85 | 1.00 | 94.2 | 402.3 | 4.27 | 4.11E-03 | 1.40E-01 | 4.27 | putative peroxidase ATP13a |
| At3g42380 | 27.1 | 6.5 | 0.24 | 1.00 | 8.2 | 34.3 | 4.15 | 5.43E-03 | 1.47E-01 | 4.15 | hypothetical protein |
| At1g63360 | 173.9 | 176.6 | 1.02 | 1.02 | 120.2 | 505.7 | 4.21 | 4.28E-03 | 1.40E-01 | 4.14 | putative zinc finger protein |
| At2g39920 | 111 | 126.3 | 1.14 | 1.14 | 130.8 | 604.9 | 4.63 | 8.84E-04 | 9.92E-02 | 4.06 | acid phosphatase class B protein |
| At5g15190 | 271.7 | 311.9 | 1.15 | 1.15 | 210.6 | 912.3 | 4.33 | 1.21E-04 | 6.91E-02 | 3.77 | putative protein |
| At4g13560 | 22 | 7.2 | 0.33 | 1.00 | 4.6 | 17.3 | 3.73 | 5.21E-04 | 8.60E-02 | 3.73 | LEA domain-containing protein |
| At1g13740 | 388.7 | 271.8 | 0.70 | 1.00 | 259.1 | 957.6 | 3.70 | 9.90E-04 | 1.02E-01 | 3.70 | expressed protein |
| At5g46230 | 384 | 314.5 | 0.82 | 1.00 | 346.2 | 1266.6 | 3.66 | 4.33E-03 | 1.41E-01 | 3.66 | expressed protein |
| At3g57010 | 112.6 | 66.4 | 0.59 | 1.00 | 63.8 | 223.4 | 3.50 | 5.54E-04 | 8.60E-02 | 3.50 | strictosidine synthase family protein |
| At5g05860 | 337.7 | 303.8 | 0.90 | 1.00 | 320.8 | 1115.9 | 3.48 | 2.19E-03 | 1.15E-01 | 3.48 | UDP-glucosyl transferase family protein |
| At2g07630 | 1.4 | 1.1 | 0.77 | 1.00 | 1 | 3.4 | 3.23 | 2.87E-03 | 1.22E-01 | 3.23 | expressed protein |
| At2g01830 | 185.6 | 199.7 | 1.08 | 1.08 | 215.7 | 712.7 | 3.30 | S.12E-04 | 9.63E-02 | 3.07 | his kinase cytokinin receptor (AHK4) |
| At3g15720 | 68 | 76 | 1.12 | 1.12 | 191 | 654.2 | 3.43 | 1.76E-03 | 1.07E-01 | 3.06 | glycoside hydrolase family 28 |
| At1g13420 | 18.8 | 4.3 | 0.23 | 1.00 | 32.1 | 97.5 | 3.04 | 8.26E-04 | 9.63E-02 | 3.04 | steroid sulfotransferase |
| At5g23270 | 38 | 49.5 | 1.30 | 1.30 | 33.3 | 128.2 | 3.85 | 3.98E-03 | 1.38E-01 | 2.96 | sugar transporter |
| At1g28100 | 190.3 | 186.4 | 0.98 | 1.00 | 186 | 543.3 | 2.92 | 1.64E-04 | 6.91E-02 | 2.92 | expressed protein |
| At1g69040 | 1368.1 | 1466.6 | 1.07 | 1.07 | 1113.5 | 3466.2 | 3.11 | 8.75E-04 | 9.92E-02 | 2.90 | ACT domain containing protein (ACR4) |
| At5g41890 | 17.4 | 4.9 | 0.28 | 1.00 | 6.2 | 17.3 | 2.79 | 2.65E-03 | 1.21E-01 | 2.79 | GDSL-motif lipase/hydrolase protein |
| At2g43550 | 537.8 | 362 | 0.67 | 1.00 | 262.2 | 698.6 | 2.66 | 1.59E-03 | 1.07E-01 | 2.66 | defensin-like family protein |
| At4g23750 | 941.7 | 1054.5 | 1.12 | 1.12 | 1337.4 | 3845.3 | 2.88 | 4.55E-04 | 8.45E-02 | 2.57 | ERF/AP2 transcription factor family |
| At1g19050 | 5149.1 | 5267.9 | 1.02 | 1.02 | 4038 | 10567.9 | 2.62 | 1.54E-04 | 6.91E-02 | 2.56 | ARR7 |
To identify genes directly activated by the ARR2ΔDDK-ER fusion, seedlings were treated (or not treated) with β-estradiol and cycloheximide (CHX) to block subsequent protein synthesis, then analyzed by Affymetrix DNA chip analysis. As a control for β-estradiol effects, CHX-treated non-transgenic seedlings were further treated or not treated with β-estradiol. Each of the treatments was duplicated, employing a total of eight DNA chips. Estimated means of the MAS 5.0 signal intensities are shown based on back-transformation of log-scale data. A two-way ANOVA was performed on log-scale data to identify genes exhibiting significant interaction between genotype (wild type vs. transgenic) and treatment (β-estradiol vs. no β-estradiol). Q-values were computed according to Storey and Tibshirani (2003). Data are sorted by the ratio of the fold change (FC) between the treated and untreated transgenic plants divided by the adjusted FC between the treated and untreated non-transgenic plants. The FC for the non-transgenic plants was adjusted to 1 for any values <1 to prevent inflation of the ratio of the FCs when the mean for the β-estradiol treated controls was less than the untreated controls.