Table III.
Top 20 genes up- and down-regulated during shoot, root, and callus development
Mean signal intensities were derived from two independent replications at each of nine different time points. Genes designated as specifically up- or down-regulated during shoot, root, or callus development, had estimated mean levels of expression at 10 d on SIM, CIM, or RIM, respectively, greater or lesser than the estimated mean levels of expression for five other comparisons as described in the text and had a q value less than or equal to 0.05 for all five comparisons. Genes were rank ordered in each developmental category by FC in expression as indicated. ca, Carpel; ce, early cotyledon; cg, green cotyledon; co, cotyledon; e, embryo; f, flower; h, hypocotyl; l, leaf; lc, cauline leaf; lm, mature leaf; lr, rosette leaf; ls, senescent leaf; ly, young, expanding leaf; pd, pedicel; pe, petiole; po, pollen; pt, petal; r, root; se, seed; sh, shoot; si, shoot internode; sn, shoot node; sp, sepal; ss, shoot seedling; st, stamen; wp, whole plant; *, data not available.
| Locus Identification | Mean Signal Intensitiesa
|
FCb | P Valuesc | q Valuesc | AtGenExpd | Gene Description | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 Time | 2 d CIM | 4 d CIM | 7 d CIM | 10 d CIM | 7 d RIM | 10 d RIM | 7 d SIM | 10 d SIM | ||||||
| Shoot up | ||||||||||||||
| At1g30040 | 59 | 2,061 | 2,529 | 6,682 | 2,391 | 1722 | 3,588 | 13,580 | 11,279 | 228.4 | 1.42E-10 | 4.93E-07 | pd, s, s, cg | GA 2-oxidase/GA2-oxidase |
| At3g19270 | 15 | 11 | 28 | 19 | 37 | 48 | 281 | 2,913 | 5,354 | 188.5 | 3.65E-04 | 1.66E-03 | sn, f, sp, sh | Cytochrome P450 |
| At1g74670 | 10 | 319 | 476 | 595 | 392 | 156 | 127 | 479 | 2,543 | 50.0 | 1.36E-05 | 2.00E-04 | l, sp, pt, l | GA-regulated protein 4 precursor |
| At3g54820 | 761 | 2,767 | 5,833 | 12,545 | 6,681 | 5,946 | 11,676 | 24,111 | 22,045 | 31.7 | 1.79E-08 | 5.77E-06 | f, f, f, sh | Aquaporin MIP-like protein |
| At1g69880 | 478 | 5,241 | 4,634 | 4,238 | 3,792 | 1,635 | 1,537 | 13,027 | 14,565 | 27.3 | 9.76E-09 | 5.06E-06 | sh, r, e, ss | Thioredoxin H-type 2 (TRX-H-2) |
| At2g40610 | 244 | 724 | 2,136 | 1,598 | 804 | 1,688 | 1,617 | 6,538 | 6,333 | 26.8 | 4.40E-06 | 1.03E-04 | f, f, pt, ly | Putative expansin (EXP8) |
| At3g13130 | 15 | 11 | 11 | 43 | 13 | 16 | 10 | 379 | 904 | 25.9 | 4.48E-04 | 1.91E-03 | *, *, *, * | Hypothetical protein |
| At5g25190 | 219 | 1,388 | 2,934 | 3,905 | 2,635 | 1,382 | 1,339 | 5,278 | 6,908 | 24.1 | 1.10E-08 | 5.06E-06 | ly, l, l, l | ERF/AP2 transcription factor subfamily B-6 |
| At2g16005 | 919 | 440 | 213 | 130 | 207 | 1,654 | 3,943 | 21,064 | 9,714 | 22.9 | 3.37E-07 | 2.32E-05 | r, r, r, r | MD-2-related lipid recognition domain-containing protein |
| At3g62950 | 4 | 4 | 8 | 5 | 4 | 7 | 5 | 70 | 119 | 16.2 | 9.30E-03 | 1.74E-02 | l, co, lm, ly | Glutaredoxin-like protein |
| At1g74890 | 214 | 134 | 203 | 310 | 28 | 56 | 71 | 3,039 | 2,656 | 14.2 | 3.28E-04 | 1.54E-03 | sh, sh, ly, h | Response regulator 15 (ARR15) |
| At5g53820 | 90 | 168 | 307 | 360 | 92 | 761 | 600 | 1,279 | 3,275 | 14.1 | 5.98E-07 | 3.21E-05 | st, po, f, f | ABA-inducible protein |
| At2g40200 | 160 | 147 | 262 | 166 | 164 | 440 | 1,347 | 2,240 | 4,377 | 14.0 | 6.54E-05 | 5.36E-04 | pd, si, si, sh | Basic helix-loop-helix (bHLH) family protein |
| At5g13330 | 1,540 | 5,003 | 6,030 | 7,495 | 4,537 | 4,115 | 6,747 | 19,560 | 23,314 | 12.7 | 3.56E-12 | 3.93E-08 | ce, cg, ce, st | ERF/AP2 transcription factor subfamily B-4 |
| At1g29090 | 111 | 75 | 206 | 115 | 66 | 111 | 153 | 1,335 | 3,550 | 12.1 | 2.88E-03 | 7.29E-03 | *, *, *, * | Peptidase C1A papain family protein |
| At3g59060 | 5 | 7 | 16 | 7 | 9 | 10 | 23 | 64 | 251 | 11.7 | 1.28E-03 | 4.01E-03 | lm, ly, lc, co | Basic helix-loop-helix (bHLH) family |
| At5g24780 | 517 | 239 | 67 | 190 | 131 | 405 | 1,026 | 5,892 | 9,905 | 11.4 | 2.05E-05 | 2.56E-04 | f, f, f, st | Vegetative storage protein 1 (VSP1) |
| At2g40670 | 186 | 286 | 162 | 31 | 11 | 50 | 137 | 2,125 | 3,222 | 11.4 | 1.28E-04 | 8.32E-04 | pt, st, st, sp | Response regulator 16 (ARR16) |
| At3g13980 | 799 | 732 | 1,403 | 1,487 | 1,191 | 3,516 | 5,990 | 8,748 | 10,156 | 10.9 | 4.88E-07 | 2.88E-05 | sn,si,h,pe | Hypothetical protein |
| At5g06870 | 80 | 140 | 381 | 1,464 | 768 | 275 | 351 | 835 | 3,360 | 10.4 | 3.18E-05 | 3.38E-04 | pe, l, pt, lm | Polygalacturonase inhibiting protein 2 (PGIP2) |
| Shoot down | ||||||||||||||
| At1g44050 | 1,016 | 588 | 279 | 45 | 67 | 181 | 202 | 43 | 14 | 0.04 | 3.01E-05 | 3.23E-04 | r, r, r, r | DC1 domain-containing protein |
| At1g80240 | 582 | 137 | 130 | 352 | 754 | 906 | 855 | 30 | 36 | 0.05 | 1.28E-04 | 8.35E-04 | r, r, r, r | Expressed protein |
| At5g50200 | 28,175 | 4,812 | 2,163 | 2,942 | 2,091 | 2,866 | 4,191 | 1,652 | 633 | 0.06 | 2.04E-06 | 6.79E-05 | r, ss, r, ss | Expressed protein |
| At1g22160 | 793 | 433 | 933 | 543 | 576 | 521 | 363 | 47 | 68 | 0.06 | 3.40E-04 | 1.58E-03 | lc, ca, f, f | Senescence-associated protein |
| At4g15400 | 1,814 | 918 | 527 | 75 | 85 | 222 | 273 | 121 | 17 | 0.07 | 6.75E-04 | 2.55E-03 | r, r, ca, r | Deacetylvindoline 4-O-acetyltransferase-like protein |
| At2g38940 | 18,789 | 1,376 | 1,263 | 1,055 | 2,183 | 2,594 | 3,685 | 1,264 | 558 | 0.07 | 1.16E-07 | 1.34E-05 | st, r, st, ss | Phosphate transporter (PT2) |
| At2g02850 | 9,273 | 21,046 | 6,326 | 1,938 | 1,661 | 6,970 | 4,949 | 626 | 742 | 0.07 | 1.30E-06 | 5.37E-05 | cg, cg, ce, ca | Plantacyanin (blue copper protein) |
| At2g21540 | 542 | 59 | 39 | 91 | 153 | 137 | 232 | 56 | 13 | 0.10 | 2.71E-04 | 1.37E-03 | po, st, st, e | Phosphoglyceride transfer protein |
| At1g55430 | 276 | 302 | 318 | 302 | 280 | 163 | 154 | 34 | 16 | 0.12 | 1.23E-02 | 2.13E-02 | r, r, r, r | DC1 domain-containing protein |
| At5g40590 | 4,895 | 5,110 | 3,906 | 1,199 | 902 | 1,977 | 1,160 | 609 | 265 | 0.12 | 9.51E-05 | 6.84E-04 | r, r, r, r | DC1 domain-containing protein |
| At3g11370 | 728 | 277 | 319 | 239 | 150 | 173 | 156 | 91 | 60 | 0.12 | 4.77E-05 | 4.36E-04 | r, r, r, r | DC1 domain-containing protein |
| At5g49780 | 823 | 295 | 216 | 107 | 89 | 94 | 204 | 113 | 27 | 0.14 | 3.94E-05 | 3.89E-04 | r, r, r, r | Leu-rich repeat transmembrane protein kinase |
| At1g48750 | 8,530 | 10,396 | 10,238 | 11,174 | 9,289 | 2,561 | 2,475 | 1,358 | 957 | 0.16 | 8.51E-07 | 4.02E-05 | f, f, ca, f | Protease inhibitor/seed storage/lipid transfer protein (LTP) |
| At1g18100 | 1,181 | 8,383 | 7,545 | 658 | 443 | 417 | 178 | 210 | 73 | 0.18 | 3.22E-05 | 3.40E-04 | se, e, e, ce | Mother of FT and TF1 protein (MFT) |
| At4g31875 | 1,870 | 3,083 | 1,080 | 1,104 | 554 | 858 | 741 | 343 | 209 | 0.18 | 2.75E-04 | 1.38E-03 | r, r, r, r | Expressed protein |
| At5g45480 | 2,827 | 696 | 914 | 1,826 | 1,771 | 1,484 | 1,682 | 533 | 473 | 0.19 | 1.88E-05 | 2.42E-04 | r, r, r, r | Expressed protein |
| At3g48080 | 833 | 442 | 334 | 861 | 474 | 213 | 206 | 163 | 113 | 0.20 | 1.20E-05 | 1.89E-04 | ls, ly, lc, lm | Lipase class 3 family protein |
| At5g59530 | 1,484 | 1,339 | 716 | 606 | 486 | 442 | 749 | 313 | 153 | 0.21 | 6.44E-05 | 5.32E-04 | r, r, r, r | 2-Oxoglutarate-dependent dioxygenase |
| At1g68810 | 1,972 | 574 | 554 | 603 | 616 | 796 | 665 | 429 | 307 | 0.22 | 1.54E-05 | 2.13E-04 | h, r, si, r | Basic helix-loop-helix (bHLH) family protein |
| At1g61360 | 2,187 | 1,100 | 835 | 1,095 | 887 | 181 | 868 | 490 | 391 | 0.22 | 1.06E-04 | 7.34E-04 | ss, r, r, r | S-locus lectin protein kinase family protein |
| Root up | ||||||||||||||
| At1g05250 | 33,194 | 785 | 162 | 134 | 281 | 8,070 | 21,606 | 2,690 | 1,271 | 49.9 | 1.24E-05 | 1.00E-03 | r, r, r, r | Peroxidase ATP12a |
| At5g38930 | 2,326 | 48 | 17 | 17 | 42 | 831 | 1,102 | 16 | 4 | 49.8 | 1.57E-03 | 1.70E-02 | sh, l, sh, r | Germin-like protein type 2 |
| At1g49860 | 12,773 | 179 | 109 | 32 | 96 | 4,751 | 4,616 | 55 | 69 | 43.8 | 7.00E-04 | 1.04E-02 | r, r, r, r | Glutathione S-transferase |
| At1g34510 | 2,479 | 24 | 19 | 12 | 155 | 752 | 3,051 | 357 | 269 | 39.8 | 2.78E-04 | 5.92E-03 | r, r, r, r | Peroxidase ATP13a |
| At3g23800 | 2,330 | 47 | 29 | 17 | 75 | 1,130 | 3,501 | 8 | 41 | 38.8 | 1.18E-03 | 1.44E-02 | r, r, r, r | Selenium-binding protein |
| At2g14900 | 3,661 | 500 | 144 | 736 | 1,701 | 5,362 | 7,729 | 2,621 | 2,487 | 37.3 | 4.94E-08 | 8.25E-05 | st, e, pt, pd | GA-regulated protein |
| At5g23020 | 16,205 | 228 | 121 | 47 | 151 | 4,266 | 9,310 | 190 | 2,059 | 35.2 | 1.62E-05 | 1.09E-03 | r, r, r, r | 2-Isopropylmalate synthase |
| At3g19710 | 21,398 | 133 | 115 | 151 | 223 | 3,566 | 5,598 | 270 | 1,632 | 31.0 | 1.49E-05 | 1.08E-03 | sn, pe, lm, h | Branched-chain amino acid aminotransferase |
| At5g53250 | 12,919 | 88 | 53 | 75 | 104 | 1,564 | 4,074 | 1,099 | 1,541 | 29.6 | 1.55E-06 | 3.46E-04 | r, r, r, r | Arabinogalactan protein |
| At4g02270 | 22,222 | 763 | 250 | 356 | 1,105 | 6,695 | 23,130 | 4,695 | 2,853 | 26.8 | 4.88E-06 | 6.12E-04 | *, *, *, * | Extensin family protein |
| At5g65530 | 1,686 | 238 | 94 | 156 | 70 | 2,219 | 2,790 | 1,215 | 1,298 | 23.6 | 7.39E-08 | 9.94E-05 | po, cg, st, ce | Putative protein kinase |
| At1g01750 | 4,781 | 43 | 69 | 62 | 132 | 1,583 | 4,668 | 956 | 839 | 23.1 | 4.86E-05 | 2.04E-03 | r, r, r, r | Actin depolymerizing factor (ADF) |
| At2g45180 | 3,752 | 161 | 204 | 242 | 375 | 4,600 | 7,334 | 643 | 1,184 | 22.6 | 5.73E-04 | 9.15E-03 | ly, ly, l, lr | Protease inhibitor/lipid transfer protein |
| At4g33730 | 2,351 | 47 | 43 | 23 | 133 | 831 | 3,269 | 776 | 567 | 19.1 | 1.58E-05 | 1.08E-03 | r, r, r, r | Pathogenesis-related protein (PR-1) |
| At5g44020 | 23,250 | 340 | 186 | 140 | 142 | 3,303 | 11,895 | 1,712 | 964 | 17.8 | 1.80E-05 | 1.17E-03 | ss, ss, ly, co | Acid phosphatase class B family protein |
| At2g32300 | 2,436 | 199 | 91 | 110 | 166 | 1,577 | 2,697 | 1,073 | 1,233 | 17.3 | 1.52E-06 | 3.46E-04 | r, r, r, r | Uclacyanin I |
| At5g15830 | 2,512 | 158 | 31 | 26 | 80 | 511 | 1,417 | 41 | 187 | 16.7 | 1.74E-04 | 4.48E-03 | lm, r, r, r | bZIP transcription factor |
| At2g27370 | 2,526 | 167 | 93 | 19 | 84 | 1,410 | 2,019 | 619 | 978 | 15.2 | 6.77E-07 | 2.64E-04 | r, r, r, r | Integral membrane protein |
| At4g14130 | 5,785 | 115 | 342 | 498 | 1,876 | 4,914 | 6,920 | 812 | 713 | 14.4 | 3.23E-06 | 5.20E-04 | r, r, r, r | Xyloglucan endotransglycosylase protein XTR-7 |
| At1g05260 | 12,728 | 430 | 254 | 492 | 477 | 3,588 | 9,862 | 3,628 | 4,257 | 14.2 | 5.25E-06 | 6.16E-04 | r, r, r, r | Peroxidase 3 (PER3) |
| Root down | ||||||||||||||
| At2g41510 | 204 | 908 | 1,001 | 1,237 | 556 | 74 | 184 | 717 | 1,422 | 0.07 | 1.64E-07 | 1.35E-04 | h, r, r, * | Cytokinin oxidase family protein |
| At5g42380 | 1,147 | 231 | 222 | 230 | 80 | 18 | 11 | 306 | 62 | 0.08 | 2.90E-04 | 6.08E-03 | r, r, h, r | Calmodulin-related protein |
| At3g28150 | 159 | 1,492 | 1,973 | 1,176 | 412 | 174 | 178 | 2,179 | 1,575 | 0.09 | 4.70E-05 | 2.00E-03 | po, st, st, se | Expressed protein |
| At1g35910 | 197 | 205 | 426 | 1,967 | 1,495 | 53 | 26 | 1,228 | 2,188 | 0.12 | 1.81E-03 | 1.87E-02 | sp, st, st, f | Rehalose-6-phosphate phosphatase |
| At2g41810 | 6,536 | 1,073 | 2,962 | 2,774 | 1,093 | 387 | 214 | 3,636 | 3,074 | 0.13 | 1.77E-03 | 1.84E-02 | r, r, *, * | Expressed protein |
| At2g14450 | 87 | 29 | 75 | 73 | 84 | 11 | 9 | 100 | 69 | 0.14 | 1.61E-02 | 7.00E-02 | *, *, *, * | Putative replication protein A1 |
| At1g77110 | 271 | 536 | 836 | 1,348 | 642 | 121 | 166 | 851 | 1,071 | 0.14 | 3.10E-03 | 2.60E-02 | f, f, f, f | Auxin transport protein (PIN6) |
| At1g61340 | 2,595 | 1,869 | 2,369 | 1,393 | 1,130 | 347 | 326 | 2,541 | 1,278 | 0.15 | 1.22E-03 | 1.46E-02 | r, r, st, ss | F-box family protein |
| At2g18470 | 19 | 510 | 816 | 1,99 | 288 | 120 | 57 | 753 | 1,058 | 0.15 | 5.80E-03 | 3.76E-02 | po, st, st, f | Protein kinase family protein |
| At1g30100 | 15 | 170 | 475 | 2,066 | 710 | 70 | 64 | 553 | 413 | 0.15 | 9.78E-03 | 5.15E-02 | cg, cg, ce, sp | 9-cis-Epoxycarotenoid dioxygenase |
| At4g25700 | 407 | 7,358 | 4,668 | 1,113 | 949 | 710 | 414 | 1,415 | 1,285 | 0.15 | 1.81E-04 | 4.56E-03 | pt, st, sp, st | β-Carotene hydroxylase |
| At1g69930 | 215 | 1,040 | 1,388 | 4,865 | 2,781 | 220 | 221 | 1,137 | 1,053 | 0.16 | 8.93E-05 | 2.87E-03 | sp, ls, ss, f | Glutathione S-transferase |
| At2g02990 | 893 | 2,454 | 4,352 | 1,272 | 2,720 | 725 | 360 | 1,190 | 791 | 0.17 | 1.30E-05 | 1.01E-03 | ce, cg, e, ce | Ribonuclease 1 (RNS1) |
| At1g71380 | 268 | 5,148 | 8,693 | 11,324 | 4,992 | 1,476 | 1,037 | 6,531 | 7,539 | 0.17 | 2.83E-07 | 1.67E-04 | po, sn, r, r | Glycosyl hydrolase family 9 protein |
| At1g03820 | 2,477 | 14,875 | 18,470 | 22,729 | 10,558 | 3,262 | 2,830 | 14,819 | 18,138 | 0.18 | 1.89E-07 | 1.46E-04 | sh, h, r, r | Expressed protein |
| At2g37770 | 141 | 1,076 | 700 | 849 | 756 | 126 | 132 | 460 | 424 | 0.18 | 5.02E-04 | 8.38E-03 | sp, sp, f, st | Aldo/keto reductase family protein |
| At5g55250 | 553 | 4,123 | 4,618 | 6,680 | 3,305 | 902 | 230 | 1,177 | 1,276 | 0.20 | 1.38E-05 | 1.04E-03 | e, e, e, e | S-Adenosyl-l-methionine:carboxyl methyltransferase protein |
| At2g41800 | 7,123 | 20,620 | 15,298 | 12,361 | 9,313 | 3,008 | 2,349 | 8,003 | 11,524 | 0.20 | 4.16E-07 | 2.17E-04 | r, ca, r, r | Expressed protein |
| At3g27400 | 427 | 10,966 | 16,651 | 21,461 | 8,234 | 3,302 | 2,370 | 17,133 | 23,630 | 0.20 | 1.46E-04 | 3.96E-03 | e, r, sn, h | Pectate lyase family protein |
| At4g27520 | 1,713 | 2,209 | 2,656 | 2,890 | 4,399 | 540 | 1,011 | 3,297 | 3,672 | 0.20 | 3.92E-05 | 1.78E-03 | lr, ly, l, ly | Plastocyanin-like domain-containing protein |
| Callus up | ||||||||||||||
| At3g60420 | 6 | 277 | 672 | 18,501 | 11,030 | 165 | 14 | 1,662 | 485 | 2982.5 | 1.49E-07 | 5.69E-06 | sp,ly,lm,sp | Expressed protein |
| At2g26400 | 245 | 485 | 2,965 | 41,945 | 44,066 | 2,716 | 620 | 9,332 | 1,160 | 171.3 | 4.52E-10 | 7.02E-07 | f,f,f,f | Acireductone dioxygenase (ARD/ARD') family protein |
| At2g04450 | 46 | 220 | 437 | 6,297 | 2,465 | 306 | 101 | 610 | 435 | 138.0 | 2.15E-08 | 2.26E-06 | wp,lm,wp,ly | MutT/nudix family protein |
| At3g57950 | 93 | 1,002 | 1,348 | 4,769 | 3,129 | 705 | 176 | 1,036 | 604 | 51.4 | 3.13E-09 | 1.25E-06 | st,r,f,st | Hypothetical protein |
| At2g45760 | 51 | 37 | 64 | 1,996 | 1,249 | 48 | 27 | 171 | 22 | 39.4 | 4.17E-04 | 9.01E-04 | r,r,r,r | BON1-associated protein 1 BAP1 |
| At4g34970 | 164 | 587 | 976 | 5,652 | 14,020 | 1,236 | 2,926 | 335 | 336 | 34.5 | 5.49E-07 | 1.14E-05 | si, pd, sn, ss | Actin-depolymerizing factor 5 (ADF-5; AtADF5) |
| At5g39110 | 378 | 95 | 51 | 8,487 | 8,400 | 1,946 | 1,307 | 1,206 | 613 | 22.4 | 5.88E-05 | 2.10E-04 | r, r, r, r | Germin-like protein |
| At1g43910 | 958 | 801 | 1,633 | 18,241 | 9,882 | 802 | 612 | 2,736 | 2,442 | 19.0 | 4.55E-09 | 1.25E-06 | pt, st, f, sp | AAA-type ATPase family protein |
| At3g56400 | 638 | 418 | 823 | 10,650 | 7,357 | 393 | 297 | 2,087 | 1,739 | 16.7 | 2.92E-07 | 8.14E-06 | ly, sp, ls, ly | Transcription factor DNA-binding protein 4 (WRKY4) |
| At1g02450 | 178 | 56 | 64 | 2,854 | 1,864 | 31 | 96 | 346 | 149 | 16.0 | 1.07E-03 | 1.89E-03 | pd, f, ca, f | NPR1/NIM1-interacting protein 1 (NIMIN-1) |
| At3g25620 | 96 | 234 | 268 | 1,455 | 991 | 214 | 69 | 219 | 120 | 15.2 | 3.44E-05 | 1.45E-04 | sn, si, st, st | ABC transporter family protein |
| At3g13630 | 225 | 168 | 331 | 3,196 | 1,528 | 171 | 210 | 191 | 224 | 14.2 | 3.73E-05 | 1.53E-04 | *, *, *, * | Hypothetical protein |
| At1g57650 | 17 | 11 | 36 | 237 | 137 | 17 | 13 | 19 | 14 | 13.6 | 1.05E-04 | 3.20E-04 | *, *, *, * | Disease resistance protein RPP1-WsA |
| At1g74710 | 495 | 256 | 490 | 6,302 | 2,845 | 371 | 274 | 1,079 | 605 | 12.7 | 1.63E-09 | 1.02E-06 | ls, sp, lm, f | Isochorismate synthase (icsI) |
| At1g19850 | 709 | 3,688 | 6501 | 8,133 | 10,930 | 6,705 | 5,747 | 7,784 | 7,500 | 11.5 | 2.07E-08 | 2.26E-06 | f, f, f, f | Transcription factor MONOPTEROS (MP) |
| At5g59060 | 35 | 22 | 139 | 392 | 619 | 146 | 174 | 108 | 10 | 11.1 | 3.72E-04 | 8.30E-04 | *, *, *, * | Expressed protein |
| At5g22570 | 291 | 104 | 159 | 3,144 | 1,712 | 201 | 157 | 297 | 237 | 10.8 | 3.28E-07 | 8.84E-06 | r, h, ly, ls | WRKY transcription factor 38 (WRKY 38) |
| At4g00750 | 70 | 148 | 211 | 655 | 1,688 | 267 | 174 | 151 | 34 | 9.3 | 2.16E-03 | 3.30E-03 | *, *, *, * | Dehydration stress ERD3 protein |
| At1g73800 | 532 | 245 | 374 | 4,738 | 2,734 | 308 | 207 | 561 | 470 | 8.9 | 7.90E-05 | 2.58E-04 | ls, wp, lm, co | Calmodulin-binding protein |
| At4g14390 | 534 | 960 | 1,495 | 4,597 | 3,700 | 1,026 | 519 | 723 | 395 | 8.6 | 1.60E-05 | 8.72E-05 | r, cg, po, lm | Ankyrin repeat family protein |
| Callus down | ||||||||||||||
| At1g73330 | 44,803 | 1,754 | 829 | 148 | 209 | 4,414 | 9,558 | 2,804 | 5,125 | 0.003 | 2.90E-08 | 2.36E-06 | r, r, r, r | Dr4 protease inhibitor |
| At1g48690 | 1,382 | 185 | 46 | 5 | 6 | 239 | 703 | 30 | 172 | 0.004 | 7.29E-08 | 3.76E-06 | r, r, r, r | Auxin-responsive GH3 family protein |
| At1g43160 | 3,186 | 328 | 31 | 14 | 5 | 49 | 838 | 188 | 276 | 0.004 | 1.18E-06 | 1.71E-05 | ce, ce, cg, r | ERF/AP2 transcription factor (subfamily B4, RAP2.6) |
| At3g44990 | 37,430 | 2,732 | 1,273 | 237 | 316 | 1,568 | 5,372 | 2,584 | 7,435 | 0.006 | 3.40E-07 | 9.03E-06 | h, r, r, lr | Xyloglucan:xyloglucosyl transferase |
| At1g60680 | 5,511 | 247 | 127 | 36 | 17 | 383 | 1,362 | 254 | 677 | 0.007 | 1.36E-05 | 7.78E-05 | cg, r, cg, r | Aldo/keto reductase family protein |
| At1g51860 | 1,529 | 762 | 271 | 15 | 18 | 233 | 787 | 170 | 81 | 0.010 | 1.97E-05 | 1.00E-04 | r, r, r, r | Leu-rich repeat protein kinase |
| At3g62040 | 6,989 | 797 | 527 | 85 | 188 | 982 | 3,809 | 518 | 841 | 0.012 | 5.27E-08 | 3.30E-06 | r, r, r, r | Haloacid dehalogenase-like hydrolase protein |
| At5g59090 | 16,582 | 1,174 | 436 | 213 | 88 | 2,648 | 6,910 | 4,400 | 11,315 | 0.013 | 8.65E-07 | 1.46E-05 | r, r, r, r | Subtilisin-like Ser protease (subtilase) |
| At5g53980 | 1,142 | 713 | 285 | 18 | 15 | 371 | 1,488 | 301 | 681 | 0.016 | 3.09E-08 | 2.46E-06 | r, r, *, * | Homeodomain Leu zipper class I (HD-Zip I) |
| At1g27030 | 8,147 | 1,526 | 1,040 | 134 | 378 | 4,686 | 8,489 | 6,785 | 8,251 | 0.016 | 1.32E-07 | 5.32E-06 | r, r, r, r | Expressed protein |
| At4g01440 | 2,836 | 716 | 478 | 47 | 20 | 754 | 917 | 237 | 205 | 0.017 | 4.21E-04 | 9.08E-04 | r, r, r, r | Nodulin MtN21 family protein |
| At5g17820 | 25,559 | 10,539 | 6,623 | 445 | 891 | 7,113 | 16,637 | 4,904 | 2,677 | 0.017 | 6.45E-06 | 4.76E-05 | r, r, r, r | Peroxidase 57 (PER57) |
| At4g12480 | 17,572 | 26,080 | 20,771 | 314 | 342 | 1,897 | 5,607 | 3,023 | 917 | 0.018 | 9.36E-09 | 1.68E-06 | lc, sh, ss, r | pEARLI 1; protease inhibitor/lipid transfer protein (LTP) |
| At2g21045 | 19,070 | 7,631 | 1,667 | 369 | 399 | 2,741 | 13,756 | 1,921 | 1,856 | 0.019 | 4.81E-08 | 3.18E-06 | r, r, r, r | Senescence-associated protein |
| At5g66390 | 6,496 | 1,773 | 313 | 129 | 159 | 2,323 | 4,822 | 1,604 | 2,383 | 0.020 | 2.53E-11 | 1.18E-07 | r, r, r, r | Peroxidase 72 (PER72) |
| At1g67330 | 9,150 | 4,544 | 1,832 | 232 | 653 | 2,724 | 5,865 | 3,471 | 3,101 | 0.025 | 3.99E-08 | 2.86E-06 | r, r, r, r | Expressed protein |
| At3g19030 | 11,251 | 2,015 | 772 | 288 | 395 | 4,398 | 9,330 | 4,229 | 4,280 | 0.026 | 1.87E-08 | 2.11E-06 | ss, ss, lm, lm | Expressed protein |
| At4g12470 | 18,137 | 25,547 | 14,123 | 562 | 429 | 1,211 | 9,030 | 1,752 | 4,743 | 0.031 | 2.77E-07 | 7.91E-06 | ss, ss, ss, h | pEARLI 1-like; protease inhibitor/lipid transfer protein (LTP) |
| At1g08325 | 4,919 | 1,167 | 783 | 164 | 104 | 960 | 2,089 | 885 | 821 | 0.033 | 3.27E-06 | 3.12E-05 | *, *, *, * | Leu zipper protein |
| At5g44530 | 1,074 | 203 | 146 | 36 | 29 | 338 | 544 | 279 | 417 | 0.034 | 5.36E-05 | 1.97E-04 | lr, e, sn, ly | subtilisin-like Ser protease (subtilase) |
a
Means from three independent replications.
b
FC for SIM 7 d/SIM 0 time, for CIM 7 d/CIM 0 time, and for RIM 7 d/RIM 4 d CIM.
c
P and q values for the comparison used in computing FC.
d
Four tissues with the highest expression levels according to the Expression Atlas of Arabidopsis Development in AtGenExpress.