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Table 3 Annotation of up- and down-regulated genes in the Ra+-Ra- library

From: Comparative transcriptional profiling-based identification of raphanusanin-inducible genes

Familya

Genome initiative No. and Putative function

Expression ratio

Function b

  

15 min

30 min

 

NTRA

AT2G17420 NTRA (NADPH-dependent thioredoxin reductase 2)

74.3 ± 11.2*

4.18 ± 1.9

1

DRP

AT4G23690 Disease resistence response protein (DRP)

33.7 ± 6.4*

9.65 ± 2*

2

ERECTA

ATG26330 Receptor Protein kinase ERECTA (ER)

10.88 ± 2.3*

15.82 ± 1*

2

CCR4-NOT

AT3G44260 CCR4-NOT transcription complex protein

4.86 ± 0.4*

3.4 ± 0.2*

3

CSN3

AB-355980 cop9 signalosome subunit 3

4.2 ± 0.7*

1.5 ± 0.3

4

Kinesin

AT2G21380 kinesin motor-protein-related

3.93 ± 0.8*

3.97 ± 1

5

UMP1

AT1G67250 Proteasome maturation factor UMP1

3.9 ± 0.6*

3 ± 0.4*

4

ACCO

X81628.1 ACC oxidase

3.67 ± 0.2*

3.96 ± 1.4

1

USP

AT3G53990 Universal stress protein (USP) family protein

1.93 ± 0.2*

2.02 ± 0.6

2

MBP 1

Y11482 Myrosinase binding protein MBP1

3.6 ± 0.5

5.1 ± 0.8*

4

KT

AT4G19960 potassium iron transporter (KT)

3.4 ± 0.9

2.24 ± 0.4*

5

CAMTA 3

AT2G22300 Calmodulin-binding transcription activator 3 (CAMTA 3)

1.65 ± 0.2

2.03 ± 0.1*

3

PTI1

AT2G30740 PTI1-like protein tyrosine kinase

2.18 ± 0.2*

3.12 ± 0.6

6

CUL1

AT4G02570 Cullin-like protein, a subunit of E3 ubiquitin ligase

2.83 ± 0.4

1.86 ± 0.2

4

SDR

AT4G09750 short-chain dehydrogenase

2.37 ± 0.3

2.2 ± 0.0.4

7

Peroxidase

AT3G32980 Heme-dependent peroxidase

5.5 ± 0.5*

3.43 ± 0.3*

1

HSP90

AT4G24190 SHD (SHEPHERD) HSP90

1.38 ± 0.3

1.26 ± 0.1

4

KEG

AT5G13530 RING E3 ligase protein (KEG)

2.13 ± 0.1*

0.8 ± 0.1

4

CIPKI

AT2G30360 SNF 1-related protein kinase

2.19 ± 0.4

2.9 ± 0.38*

6

GH3

AT5G20950 Glycosyl hydrolase family 3 protein(GH3)

2.1 ± 0.3

1.4 ± 0.1

7

CESA5

AT5G09870 Cellulose synthase 5- transferase

1.5 ± 0.1

1.95 ± 0.1*

5

CAT2

AF139538 Catalase2

1.97 ± 0.2*

1.6 ± 0.3

1

Glycoprotein

AT1G14710 Hydroxy proline rich glycoprotein family

1.88 ± 0.2*

0.9 ± 0.1

10

POT

AT3G16180 Proton-dependent oligopeptide transport (POT) family protein

1.82 ± 0.1*

1.05 ± 0.1

5

LRT

AT2G31880 Leucine-rich repeat tranmemberane protein kinase

1.91 ± 0.5

1.7 ± 0.2

6

Clathrin

AT1G60780 Clathrin adaptor complexs medium subunit family protein

1.8 ± 0.14*

1.2 ± 0.1

5

PKC

AY835401.1 Protein Kinase C conserved region 2

1.7 ± 0.2

0.38 ± 0.1*

6

Pescadillo

AT5G14520 Pescadillo-related protein

1.7 ± 0.2

2.12 ± 0.4

3

3KCS4

AT1G19440 Very long-chain fatty acid condensing enzyme

1.6 ± 0.1

1.5 ± 0.2

5

Profilin

AT2G19760 Profilin1

1.59 ± 0.1

2.23 ± 0.1*

9

Dehydrin

AT2G39750 Dehydration-responsive family protein

1.67 ± 0.2

1.8 ± 0.3

10

PGβ1

AT1G70370 Polygalacturonase isoenzyme 1 beta subunit homolog

1.56 ± 0.2

1.44 ± 0.2

10

MAK

AT5G45430 serine/threonine-protein kinase Mak

1.6 ± 0.3

1.25 ± 0.1

6

3PGDH

AT1G17745 3-phosphoglycerate dehydrogenase

1.65 ± 0.1*

1.8 ± 0.2

7

Ring Finger

AT3G09760 C3HC4-type Ring Finger

1.55 ± 0.2

1.92 ± 0.1*

4

G6PDH

AT5G35790 Glucose 6 -phosphate dehydrogenase

0.69 ± 0.1

1.6 ± 0.2

7

GTPase

AT5G53570 Gtpase activator protein for Rab-like GTPase-like protein

1.5 ± 0.1

2 ± 0.2

2

UBQ3

At5g03240 UBQ3

1.4 ± 0.1

2.35 ± 0.2*

4

CND41

AT3G18490 aspartyl protease family protein

1.3 ± 0.1

0.01 ± 0.1*

4

MetE

AT5G17920 Cobalamin-independent methionine synthase

1.4 ± 0.1

1.13 ± 0.1

4

RALF

AT3G16570 Rapid Alkalization Factor 23 (RALF23)

1.31 ± 0.2

2.3 ± 0.4

2

PPEase

AT2G26870 Phosphoesterase family protein

1.3 ± 0.1

1.3 ± 0.1

7

CPOX

AF375424 Coproporphyrinogen III oxidase

1.3 ± 0.1

1.45 ± 0.1

1

BURP

AT1G70370 Polygalacturonase isoenzyme 1 beta subunit homolog

1.3 ± 0.1

1.1 ± 0.1

10

GASA4

AT5G15230 GASA4 (GAST1 protein homolog)

1.27 ± 0.2

3.1 ± 0.7

10

PLC

AAD26119.1 Phosphoinositide- specific phospholipase C

1.23 ± 0.1

1.78 ± 0.2

2

MAG2

AT3G47700 MAG2(chromosome structure maintenance protein-related)

1.2 ± 0.1

1.7 ± 0.1*

5

GTF

AT1G19710 Glycosyl transferase family 1 protein

1.07 ± 0.1

1.95 ± 0.1*

5

RMB2

AB042187 Myrosinase (RMB2)

0.45 ± 0.1

1.66 ± 0.1*

7

RMB1

AB04218 Myrosinase (RMB1)

0.52 ± 0.1

1.52 ± 0.2

7

  1. a one representative clone for each gene is shown. Three independent biological replicates were performed. Value ± s.e. indicates expression ratio of Treatment/Control after normalization ± standard error of the mean (n = 3).Genes in the table are listed in decreasing expression ratios according to genes in the Ra+-Ra- library. Genes that differ significantly (student t test p-value less than 0.05) in their expression between the treatment and control are marked with an asterisk (*). Bold represents the expression ratios (≥ 1.5 or ≤ 0.6). bThe functional categories are, 1: Oxidase, 2: signal tranduction, 3: transcription and translation, 4: protein metabolism/binding, 5: movement and transport, 6: kinases, 7: Hydrolases, 8: Energy, 9: Cellular biogenesis, 10: Unclassified. The values shown represent fold change (treatment vs. control).