Skip to main content

Table 2 Organ-specificity of genes differentially expressed in cytokinin-deficient plants

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

Category CATMA ID AbB Ratio CKX1 vs. Col-0 FDR p-value genotype effect AGI Description
    Root Shoot    
root-specific CATMA5a61330 11 18.32 1.26 7.99E-04 AT5G65990 amino acid transporter family protein
  CATMA3a43475 5 7.63 1.57 9.62E-06 AT3G50410 Dof-type zinc finger domain-containing protein
  CATMA1a62410 4 5.66 0.63 4.99E-02 AT1G73165 Clavata3 / ESR-Related-1 (CLE1)
  CATMA5a37900 7 4.72 1.07 4.77E-03 AT5G42200 zinc finger (C3HC4-type RING finger) family protein
  CATMA3a40595 4 2.86 0.97 5.65E-03 AT3G47600 myb family transcription factor (MYB94)
  CATMA1a66990 9 2.60 0.89 5.31E-03 AT1G77840 eukaryotic translation initiation factor 5, putative (eIF-5)
  CATMA4a36496 11 0.27 1.10 1.04E-02 AT4G34680 GATA transcription factor 3, putative (GATA-3)
  CATMA2a45310 4 0.02 1.03 1.77E-02 AT2G46870 DNA-binding protein, putative
shoot-specific CATMA4a00090 9 1.00 76.53 1.19E-03 AT4G00080 invertase/pectin methylesterase inhibitor family protein
  CATMA5a49170 9 1.33 15.44 4.78E-03 AT5G53250 arabinogalactan-protein, putative (AGP22)
  CATMA4a26210 10 1.46 12.59 1.52E-06 AT4G24480 serine/threonine protein kinase, putative
  CATMA4a02865 9 1.01 8.82 2.70E-03 AT4G02560 homeobox protein LUMINIDEPENDENS (LD)
  CATMA3a15410 4 0.55 8.43 1.83E-02 AT3G15990 sulfate transporter, putative
  CATMA2a44715 11 1.63 4.29 4.50E-04 AT2G46340 phytochrome A supressor spa1 (SPA1)
  CATMA2a31150 13 0.68 3.08 1.72E-02 AT2G32950 COP1 regulatory protein
  CATMA2a00475 14 1.07 0.38 2.37E-02 AT2G01420 auxin transport protein, putative
  CATMA1a08416 13 0.81 0.33 2.02E-02 AT1G09570 phytochrome A (PHYA)
  CATMA3a19415 16 1.24 0.33 2.33E-02 AT3G19820 cell elongation protein DWARF1 / DIMINUTO (DWF1/DIM)
  CATMA5a06800 13 0.59 0.20 2.63E-05 AT5G07580 ERF subfamily B-3 of ERF/AP2 transcription factor
  CATMA4a18523 10 0.72 0.20 2.23E-03 AT4G17490 ERF subfamily B-3 of ERF/AP2 transcription factor (ATERF-6)
  CATMA2a32570 16 0.69 0.18 1.82E-03 AT2G34420 chlorophyll A-B binding protein (LHB1B2)
  CATMA4a36460 15 0.99 0.17 3.19E-03 AT4G34620 ribosomal protein S16 family protein
  CATMA2a24825 13 1.86 0.16 1.26E-02 AT2G26500 cytochrome b6f complex subunit (petM), putative
  CATMA5a60355 12 0.41 0.15 2.94E-06 AT5G64920 COP1-interacting protein (CIP8)
  CATMA4a22880 9 1.10 0.15 4.50E-03 AT4G21280 PsbQ subunit of photosystem II
  CATMA5a59535 4 0.59 0.12 1.99E-04 AT5G64040 photosystem I reaction center subunit PSI-N
  CATMA1a68150 7 0.70 0.11 8.69E-03 AT1G79040 10 kDa PsbR subunit of photosystem II (PSII)
  CATMA5a43205 16 0.63 0.11 1.37E-05 AT5G47220 ERF subfamily B-3 of ERF/AP2 transcription factor (ATERF-2)
  CATMA1a68150 7 0.70 0.11 8.69E-03 AT1G79040 10 kDa PsbR subunit of photosystem II
  CATMA1a46750 13 1.38 0.06 3.91E-03 AT1G55670 photosystem I reaction center subunit V
  CATMA5a43215 15 0.78 0.05 7.70E-04 AT5G47230 ERF subfamily B-3 of ERF/AP2 transcription factor (ATERF-5)
  CATMA2a43300 11 0.52 0.04 9.62E-06 AT2G44840 ERF subfamily B-3 of ERF/AP2 transcription factor
  CATMA5a57200 11 0.64 0.03 3.30E-03 AT5G61600 ERF subfamily B-3 of ERF/AP2 transcription factor
  CATMA5a47120 7 0.42 0.03 1.20E-03 AT5G51190 ERF subfamily B-3 of ERF/AP2 transcription factor
similar CATMA5a07985 10 16.98 57.30 3.42E-03 AT5G08640 flavonol synthase 1 (FLS1)
  CATMA4a10345 8 24.01 16.17 1.99E-03 AT4G10310 sodium transporter (HKT1)
  CATMA5a52815 11 3.38 33.99 5.78E-05 AT5G57090 auxin transport protein (EIR1) (PIN2)
  CATMA2a45915 8 4.11 26.54 5.82E-04 AT2G47460 subgroup 7 of R2R3-MYB family (MYB12)
  CATMA2a32640 11 3.20 25.43 2.07E-04 AT2G34500 cytochrome P450 family protein
  CATMA1a04035 5 3.86 5.95 1.72E-02 AT1G05180 auxin-resistance protein (AXR1)
  CATMA5a12150 15 3.65 4.48 2.57E-04 AT5G13930 chalcone synthase
  CATMA3a11725 8 4.38 3.17 1.42E-02 AT3G12750 zinc transporter (ZIP1)
  CATMA3a54340 14 0.34 0.29 2.75E-02 AT3G61190 BON1-associated protein 1 (BAP1)
  CATMA1a26550 4 0.34 0.26 9.57E-06 AT1G28370 ERF subfamily B-1 of ERF/AP2 transcription factor
  CATMA1a09322 10 0.30 0.29 1.19E-03 AT1G10470 response regulator 4 (ARR4)
  CATMA3a16175 16 0.17 0.38 3.92E-03 AT3G16770 ERF subfamily B-2 of ERF/AP2 transcription factor (RAP2.3)
  CATMA5a04585 11 0.21 0.31 7.30E-03 AT5G05410 DREB subfamily A-2 of ERF/AP2 transcription factor (DREB2A)
  CATMA3a14565 15 0.26 0.20 4.00E-03 AT3G15210 ERF subfamily B-1 of ERF/AP2 transcription factor (ATERF-4)
  CATMA5a58475 5 0.11 0.29 6.22E-04 AT5G62920 response regulator (ARR6)
  CATMA1a66910 8 0.28 0.09 7.72E-04 AT1G77760 nitrate reductase 1 (NR1)
  CATMA1a57435 6 0.12 0.18 1.18E-03 AT1G68050 F-box family protein (FKF1) / adagio 3 (ADO3)
  CATMA1b35155 7 0.19 0.05 8.13E-04 AT1G37130 nitrate reductase 2 (NR2)
  1. The table contains an arbitrary selection of genes showing altered transcript abundance under cytokinin deficiency. A number of these genes are discussed in the text. The categorization was performed as described in Methods and in Additional file 1: Figure S1. Expression ratios in roots and shoots of cytokinin-deficient seedlings relative to the wild-type control are given and coded by font variants: bold, upregulation; italics, downregulation; regular, no regulation. 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. FDR corrected p-values ≤ 0.03, indicating whether a gene was significantly regulated by cytokinin, are marked with bold numbers.