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Table 3 Genes indicative of a developmental shift due to an altered cytokinin status

From: Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses

CATMA ID AbB Ratio FDR p-value AGI Subcellular localization Description
   BA1080 vs. BA0 Root CKX1 vs. BA0 Shoot Root vs. Shoot @ BA0 Cytokinin effect Organ effect Interaction effect    
CATMA2a26583 40 2.71 0.09 0.04 5.78E-07 3.27E-11 1.12E-06 AT2G28190 a,P superoxide dismutase (Cu-Zn) (SODCP)
CATMA5a16150 35 2.80 0.09 0.03 1.83E-06 5.98E-18 2.95E-05 AT5G17870 P plastid-specific ribosomal protein-related
CATMA3a44603 29 2.71 0.12 0.00 4.68E-03 2.58E-21 5.67E-05 AT3G51600 w nonspecific lipid transfer protein 5 (LTP5)
CATMA1a65310 37 4.44 0.14 0.01 3.01E-11 1.64E-29 2.54E-10 AT1G76080 P thioredoxin family protein
CATMA2a35500 34 3.08 0.13 0.07 2.34E-06 5.32E-13 2.70E-04 AT2G37220 P 29 kDa ribonucleoprotein
CATMA1a13920 37 2.76 0.13 0.20 8.52E-05 7.32E-05 4.18E-04 AT1G14890 invertase/pectin methylesterase inhibitor family protein
CATMA1a19333 37 3.21 0.14 0.01 3.04E-06 6.27E-22 9.90E-06 AT1G20340 P plastocyanin
CATMA4a22880 23 2.73 0.14 0.01 3.41E-06 5.25E-25 7.49E-06 AT4G21280 P PsbQ subunit of photosystem II
CATMA2a04295 38 2.74 0.15 0.03 8.82E-04 3.72E-19 6.27E-06 AT2G05520 e glycine-rich protein (GRP)
CATMA5a07300 33 6.42 0.35 0.01 5.78E-05 2.59E-21 1.92E-06 AT5G08050 P expressed protein
CATMA5a12555 27 3.74 0.18 0.02 8.15E-06 1.76E-21 2.42E-06 AT5G14320 P 30S ribosomal protein S13, chloroplast (CS13)
CATMA4a30310 36 5.11 0.25 0.01 3.41E-06 6.23E-24 4.24E-06 AT4G28660 P photosystem II reaction centre W (PsbW) family protein
CATMA3b54606 36 2.96 0.17 0.01 2.16E-02 1.77E-21 5.67E-05 AT3G61470 P chlorophyll A-B binding protein (LHCA2)
CATMA3a14550 40 3.01 0.19 0.04 7.16E-06 4.96E-20 3.23E-04 AT3G15190 P chloroplast 30S ribosomal protein S20
CATMA2a41430 36 3.74 0.22 0.04 3.50E-05 4.69E-18 2.18E-04 AT2G43030 P ribosomal protein L3 family protein
CATMA4a26750 18 2.92 0.19 0.03 1.59E-05 2.30E-20 8.52E-05 AT4G25050 P acyl carrier protein predominantly expressed in leaves
CATMA2a35140 30 3.69 0.23 0.03 2.86E-05 4.06E-18 9.10E-04 AT2G36870 a,e,w xyloglucan:xyloglucosyl transferase
CATMA1a63880 31 3.32 0.22 0.04 7.39E-04 2.67E-18 9.61E-05 AT1G74470 P geranylgeranyl reductase
CATMA4a18000 32 4.95 0.35 0.01 2.52E-06 1.37E-22 8.09E-06 AT4G16980 e arabinogalactan-protein family
CATMA5a51450 30 2.74 0.20 0.05 1.20E-03 8.97E-17 7.88E-05 AT5G55700 P similar to beta-amylase (CT-BMY)
CATMA4a40410 32 2.58 0.19 0.01 1.30E-05 8.94E-23 1.90E-04 AT4G38970 a,P fructose-bisphosphate aldolase
CATMA2a37967 40 2.68 0.20 0.02 1.15E-05 2.09E-22 3.60E-05 AT2G39730 a,n,P,w RuBisCO activase
CATMA1a36300 39 3.16 0.23 0.01 2.11E-04 1.04E-22 8.53E-05 AT1G42970 a,P glyceraldehyde-3-phosphate dehydrogenase B (GAPB)
CATMA1a27050 40 4.20 0.29 0.03 6.60E-07 4.24E-22 7.68E-06 AT1G29070 P ribosomal protein L34 family protein
CATMA1a64335 34 4.00 0.29 0.03 8.82E-06 1.17E-20 1.03E-05 AT1G74970 P ribosomal protein S9 (RPS9)
CATMA5a36620 34 4.23 0.32 0.03 3.06E-05 3.96E-21 7.34E-06 AT5G40950 P 50S ribosomal protein L27, chloroplast (RPL27)
CATMA5a39880 34 3.01 0.23 0.07 8.93E-05 1.17E-15 1.19E-07 AT5G44130 w,p fasciclin-like arabinogalactan-protein
CATMA1a13350 28 3.28 0.26 0.01 1.31E-05 3.61E-19 6.76E-05 AT1G14345 P expressed protein, one transmembrane domain
CATMA3a11290 38 2.98 0.25 0.02 2.46E-05 5.34E-22 6.59E-05 AT3G12340 P immunophilin-related
CATMA4a01510 23 2.96 0.25 0.06 2.93E-05 1.70E-18 1.06E-03 AT4G01310 c,P ribosomal protein L5 family protein
CATMA4a23520 29 3.77 0.32 0.05 5.33E-02 1.68E-12 8.70E-05 AT4G21860 P methionine sulfoxide reductase domain protein
CATMA4a26465 34 4.05 0.35 0.05 2.79E-05 7.36E-18 4.05E-04 AT4G24770 P 31 kDa ribonucleoprotein
CATMA1a60820 32 3.12 0.27 0.03 2.10E-02 3.18E-19 8.43E-05 AT1G71500 P Rieske (2Fe-2S) domain-containing protein
CATMA4a17230 37 3.28 0.30 0.03 5.81E-05 1.22E-19 6.59E-05 AT4G16410 expressed protein
CATMA2a00475 32 3.43 0.35 0.20 1.16E-04 1.64E-10 3.85E-05 AT2G01420 auxin transport protein
CATMA4a21620 29 2.96 0.30 0.06 3.23E-04 2.54E-19 8.87E-05 AT4G20360 a,n,P elongation factor Tu (TUFA)
CATMA1a00590 36 2.96 0.32 0.11 5.48E-05 1.14E-15 1.85E-07 AT1G01610 glycerol-3-phosphate acyltransferase
CATMA1a67690 35 2.73 0.29 0.04 2.94E-03 1.49E-20 8.53E-05 AT1G78630 P ribosomal protein L13 family protein
CATMA1a67475 33 3.48 0.39 0.23 1.49E-05 5.10E-08 3.19E-04 AT1G78380 c,P,p,v glutathione S-transferase, putative
CATMA2a30900 35 2.63 0.31 0.08 1.43E-05 2.00E-17 1.10E-02 AT2G32180 P expressed protein
CATMA3a20410 34 2.69 0.32 0.10 8.23E-06 8.91E-16 8.79E-05 AT3G20680 P expressed protein
CATMA5a19250 39 2.55 0.32 0.17 3.50E-04 4.39E-14 8.94E-05 AT5G20720 a,M,P 20 kDa chaperonin (CPN21)
CATMA3a52950 31 2.72 0.36 0.21 4.03E-05 7.38E-12 6.45E-05 AT3G59940 kelch repeat-containing F-box family protein
CATMA1a30400 31 2.66 0.36 0.01 5.00E-05 1.33E-23 5.57E-03 AT1G32060 a,P phosphoribulokinase (PRK)
CATMA5a43410 23 0.00 17.15 278.19 4.95E-09 2.53E-13 0.046445 AT5G47450 v major intrinsic family protein
CATMA3a46940 19 0.02 10.04 116.88 7.21E-06 6.92E-12 0.024062 AT3G53980 e lipid transfer protein (LTP) family protein
CATMA3a00185 23 0.08 12.14 141.58 1.49E-08 8.53E-21 6.09E-06 AT3G01190 e peroxidase 27 (PER27)
CATMA3a23750 16 0.11 25.69 233.14 1.38E-05 4.82E-16 0.00675 AT3G23800 selenium-binding family protein
CATMA1a40940 11 0.14 17.74 11.32 2.3E-05 1.52E-05 0.011573 AT1G49860 c glutathione S-transferase
CATMA1a28300 19 0.24 4.60 11.59 5.14E-05 2.23E-08 0.021175 AT1G30270 c,n,p CBL-interacting protein kinase 23 (CIPK23)
CATMA5a08890 20 0.24 32.72 56.89 2.23E-10 6.53E-18 2.93E-05 AT5G10130 e,x pollen Ole e 1 allergen and extensin family protein
CATMA2a25985 17 0.26 11.72 28.97 5.25E-06 7.78E-13 0.473892 AT2G27550 centroradialis protein (CEN)
CATMA1a22610 22 0.28 36.53 105.82 7.83E-06 4.44E-15 0.000233 AT1G23720 w proline-rich extensin-like family protein
CATMA3a23170 25 0.29 13.03 75.65 7.07E-07 3.96E-21 1.58E-06 AT3G23175 E lesion inducing protein-related
CATMA1a61170 22 0.30 2.78 3.42 8.77E-07 1.88E-07 0.468587 AT1G71960 p ABC transporter family protein
CATMA2a37070 24 0.31 11.75 27.66 7.75E-05 3.99E-13 0.000278 AT2G38800 calmodulin-binding protein-related
CATMA1a44600 16 0.31 4.16 4.65 4.64E-05 1.63E-05 0.014032 AT1G53590 v C2 domain-containing protein
CATMA4a10345 14 0.34 17.87 38.52 3.41E-06 2.36E-10 0.071489 AT4G10310 p sodium transporter (HKT1)
CATMA5a06070 27 0.34 2.56 3.11 3.47E-08 1.77E-11 0.307964 AT5G06850 C2 domain-containing protein
CATMA1a04113 20 0.35 2.71 21.16 2.8E-05 8.54E-17 0.079992 AT1G05260 E peroxidase 3 (PER3)
CATMA1a28520 23 0.36 5.05 5.28 3.41E-06 4E-11 2.69E-05 AT1G30510 P ferredoxin--NADP(+) reductase
CATMA3a48230 23 0.37 7.91 20.28 2.97E-06 5.49E-15 0.027924 AT3G55230 e disease resistance-responsive family protein
CATMA5a09320 11 0.37 5.73 13.92 4.28E-08 1.53E-17 2.74E-05 AT5G10580 e expressed protein
  1. The table shows a list of genes, which have both a more shoot-like transcript level in long-term cytokinin-treated roots (Additional file 4: Table S3) and a more root-like transcript level in cytokinin-deficient shoots (Additional file 8: Table S4). Expression ratios are given for long-term cytokinin-treated roots and for cytokinin-deficient shoots in comparison to the mock-treated wild-type samples, as well as for the difference between roots and shoots. The expression ratios are coded: by different font variants: bold, up-regulation; italic, downregulation, regular, no regulation. The FDR-corrected p-values for the cytokinin effect indicate whether a gene was significantly regulated by cytokinin. The FDR-corrected p-values for the organ effect indicate whether the expression level of a gene was significantly different in roots and shoots. The FDR-corrected p-value for the interaction effect indicates whether cytokinin-dependent gene regulation was dependent on the organ. FDR-corrected p-values ≤ 0.03 were regarded as significant and marked with bold numbers. CATMA ID, unique identifier for the gene specific tag (probe) on the microarray (data can be queried under http://www.catma.org); AbB, number of spots above background (a rough measure for expression strength); AGI, unique gene identifier assigned by TAIR; Description, edited TAIR database annotation. Abbreviations for the subcellular localization are: a, apoplast; c, cytosol; E, endoplasmatic reticulum; e, endomembrane system; M, mitochondrium; n, nucleus; P, plastid; p, plasma membrane; v, vacuole; w, cell wall; x, extracellular space; —, not available or unknown.