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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.
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BMC Plant Biology

ISSN: 1471-2229

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