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