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Table 3 135 genes with predicted root-enrichment expression profiles by Audic-Claverie statistic

From: Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis viniferaL.) based on curation and mining of large-scale EST data sets

Gene ID

Gene Description

Gene Function (via VitisNet)

Root EST count (frequency)

Non-root EST count (frequency)

AC statistic

GSVIVP00030165001

Lectin

7.0 Stress-related

68 (40.1)

32 (1.2)

< 1E-06

GSVIVP00027836001

Curculin (mannose-binding) lectin

6.0 Binding

59 (34.8)

5 (0.2)

< 1E-06

GSVIVP00024394001

Aquaporin TIP1;4

5.3 Transport System

57 (33.6)

2 (0.1)

< 1E-06

GSVIVP00029248001

Aquaporin TMP-C

5.3 Transport System

57 (33.6)

15 (0.6)

< 1E-06

GSVIVP00015118001

Aspartic proteinase nepenthesin-1

2.3 Folding, Sorting & Degradation

47 (27.7)

38 (1.4)

< 1E-06

GSVIVP00036222001

Endochitinase 1, basic

1.0 Primary Metabolism

33 (19.5)

1 (0.1)

< 1E-06

GSVIVP00032953001

Glutamine synthetase (cytosolic) 2

1.2 Energy Metabolism

32 (18.9)

26 (1)

< 1E-06

GSVIVP00018661001

Resveratrol O-methyltransferase

1.9 Secondary Metabolism

30 (17.7)

0 (0)

< 1E-06

GSVIVP00013365001

Mannitol dehydrogenase

1.0 Primary Metabolism

26 (15.3)

26 (1)

< 1E-06

GSVIVP00006171001

Phosphate-induced protein 1

Unclear

26 (15.3)

37 (1.4)

< 1E-06

GSVIVP00015200001

Phosphate-induced protein 1

Unclear

24 (14.2)

5 (0.2)

< 1E-06

GSVIVP00027842001

(E,E)-alpha-Farnesene synthase

1.9 Secondary Metabolism

23 (13.6)

0 (0)

< 1E-06

GSVIVP00004164001

IAA beta-glucosyltransferase

3.2 Hormone Signaling

20 (11.8)

1 (0.1)

< 1E-06

GSVIVP00037746001

C2 domain-containing

3.1 Signal Transduction

20 (11.8)

7 (0.3)

< 1E-06

GSVIVP00036564001

Carboxylesterase

1.0 Primary Metabolism

19 (11.2)

0 (0)

< 1E-06

GSVIVP00011776001

Polyphenol oxidase II, chloroplast

5.3 Transport System

19 (11.2)

17 (0.7)

< 1E-06

GSVIVP00020241001

Unknown

Unknown

19 (11.2)

30 (1.1)

< 1E-06

GSVIVP00013172001

Octicosapeptide/Phox/Bem1p (PB1)

Unknown

18 (10.6)

12 (0.5)

< 1E-06

GSVIVP00030638001

Xyloglucan endotransglycosylase

4.3 Cell Wall

18 (10.6)

28 (1)

< 1E-06

GSVIVP00036411001

RD22

7.0 Stress-related

17 (10)

5 (0.2)

< 1E-06

GSVIVP00021415001

Glutathione S-transferase 8

1.0 Primary Metabolism

16 (9.4)

14 (0.5)

< 1E-06

GSVIVP00009226001

Stilbene synthase

1.9 Secondary Metabolism

15 (8.8)

7 (0.3)

< 1E-06

GSVIVP00017772001

ATP synthase beta chain 2

5.3 Transport System

15 (8.8)

18 (0.7)

< 1E-06

GSVIVP00025990001

Caffeic acid O-methyltransferase

1.9 Secondary Metabolism

14 (8.3)

22 (0.8)

< 1E-06

GSVIVP00011267001

Flavonol sulfotransferase

1.9 Secondary Metabolism

13 (7.7)

0 (0)

< 1E-06

GSVIVP00002185001

DNA-binding protein

2.4 Replication & Repair

13 (7.7)

1 (0.1)

< 1E-06

GSVIVP00036600001

Nitrite reductase

1.2 Energy Metabolism

13 (7.7)

5 (0.2)

< 1E-06

GSVIVP00034550001

Unknown protein

Unknown

13 (7.7)

7 (0.3)

< 1E-06

GSVIVP00018662001

Orcinol O-methyltransferase 2

1.9 Secondary Metabolism

12 (7.1)

0 (0)

< 1E-06

GSVIVP00022812001

Germin

8.0 Storage

12 (7.1)

0 (0)

< 1E-06

GSVIVP00019908001

7S globulin precursor, basic

2.3 Folding, Sorting & Degradation

12 (7.1)

4 (0.2)

< 1E-06

GSVIVP00021582001

E8 protein

3.2 Hormone Signaling

12 (7.1)

4 (0.2)

< 1E-06

GSVIVP00013571001

Strictosidine synthase

1.9 Secondary Metabolism

12 (7.1)

5 (0.2)

< 1E-06

GSVIVP00020905001

Aldose 1-epimerase

1.0 Primary Metabolism

12 (7.1)

10 (0.4)

< 1E-06

GSVIVP00002589001

Unknown protein

Unknown

12 (7.1)

11 (0.4)

< 1E-06

GSVIVP00004581001

Carboxyesterase 20

1.0 Primary Metabolism

11 (6.5)

1 (0.1)

< 1E-06

GSVIVP00027736001

4-Amino-4-deoxychorismate lyase

1.0 Primary Metabolism

11 (6.5)

1 (0.1)

< 1E-06

GSVIVP00036840001

Ferulate-5-hydroxylase

1.9 Secondary Metabolism

11 (6.5)

3 (0.1)

< 1E-06

GSVIVP00001860001

UDP-glucose:anthocyanidin 5,3-O-glucosyltransferase

1.9 Secondary Metabolism

11 (6.5)

4 (0.2)

< 1E-06

GSVIVP00032824001

Aspartic proteinase nepenthesin-2

2.3 Folding, Sorting & Degradation

11 (6.5)

4 (0.2)

< 1E-06

GSVIVP00023389001

WRKY DNA-binding protein 11

2.11 Transcription Factors

11 (6.5)

6 (0.3)

< 1E-06

GSVIVP00031491001

UDP-glucose glucosyltransferase

1.0 Primary Metabolism

10 (5.9)

1 (0.1)

< 1E-06

GSVIVP00037558001

Flavonol O-glucosyltransferase

1.9 Secondary Metabolism

10 (5.9)

1 (0.1)

< 1E-06

GSVIVP00036143001

Monooxygenase

Unclear

10 (5.9)

1 (0.1)

< 1E-06

GSVIVP00017017001

Trans-cinnamate 4-monooxygenase

1.9 Secondary Metabolism

10 (5.9)

2 (0.1)

< 1E-06

GSVIVP00033062001

Senescence-associated gene (SAG101)

4.2 Cell Growth & Death

10 (5.9)

3 (0.1)

< 1E-06

GSVIVP00018298001

Phosphate translocator protein2, plastid

5.3 Transport System

10 (5.9)

7 (0.3)

< 1E-06

GSVIVP00005745001

Octicosapeptide/Phox/Bem1p (PB1) domain

Unknown

10 (5.9)

13 (0.5)

< 1E-06

GSVIVP00005849001

Anthocyanidin 3-O-glucosyltransferase

1.9 Secondary Metabolism

10 (5.9)

16 (0.6)

< 1E-06

GSVIVP00036485001

CYP82C4

1.0 Primary Metabolism

9 (5.3)

1 (0.1)

< 1E-06

GSVIVP00002954001

Cinnamyl-alcohol dehydrogenase

1.9 Secondary Metabolism

9 (5.3)

1 (0.1)

< 1E-06

GSVIVP00031199001

Cytokinin-O-glucosyltransferase 2

1.9 Secondary Metabolism

9 (5.3)

3 (0.1)

< 1E-06

GSVIVP00015320001

Nitrate reductase 2 (NR2)

3.1 Signal Transduction

9 (5.3)

3 (0.1)

< 1E-06

GSVIVP00025346001

beta-1,3-Glucanase

1.0 Primary Metabolism

9 (5.3)

4 (0.2)

< 1E-06

GSVIVP00013928001

Phenylalanine ammonia-lyase

1.9 Secondary Metabolism

9 (5.3)

8 (0.3)

< 1E-06

GSVIVP00005194001

Stilbene synthase

1.9 Secondary Metabolism

9 (5.3)

8 (0.3)

< 1E-06

GSVIVP00001453001

Salt tolerance zinc finger

2.11 Transcription Factors

9 (5.3)

11 (0.4)

< 1E-06

GSVIVP00037055001

Metal-nicotianamine transporter YSL7

5.3 Transport System

9 (5.3)

11 (0.4)

< 1E-06

GSVIVP00020070001

Sulfate adenylyltransferase 3

1.2 Energy Metabolism

9 (5.3)

13 (0.5)

< 1E-06

GSVIVP00000463001

Cinnamyl alcohol dehydrogenase

1.9 Secondary Metabolism

9 (5.3)

14 (0.5)

< 1E-06

GSVIVP00024717001

Peroxidase

1.0 Primary Metabolism

8 (4.7)

0 (0)

< 1E-06

GSVIVP00031214001

Cytokinin-O-glucosyltransferase 2

1.9 Secondary Metabolism

8 (4.7)

0 (0)

< 1E-06

GSVIVP00034489001

2-Oxoglutarate-dependent dioxygenase

Unclear

8 (4.7)

0 (0)

< 1E-06

GSVIVP00036965001

Glutathione S-transferase 10 GSTU10

1.0 Primary Metabolism

8 (4.7)

1 (0.1)

< 1E-06

GSVIVP00018322001

Glucosyltransferase-2

1.0 Primary Metabolism

8 (4.7)

2 (0.1)

< 1E-06

GSVIVP00019233001

Isoflavone reductase

1.9 Secondary Metabolism

8 (4.7)

2 (0.1)

< 1E-06

GSVIVP00029527001

Unknown protein

Unknown

8 (4.7)

2 (0.1)

< 1E-06

GSVIVP00003722001

Zinc finger (C3HC4-type RING finger)

2.11 Transcription Factors

8 (4.7)

3 (0.1)

< 1E-06

GSVIVP00010417001

Zinc finger (C3HC4-type RING finger)

6.0 Binding

8 (4.7)

5 (0.2)

< 1E-06

GSVIVP00034781001

Kelch repeat-containing F-box

Unknown

8 (4.7)

5 (0.2)

< 1E-06

GSVIVP00020913001

Aldose 1-epimerase

1.0 Primary Metabolism

8 (4.7)

6 (0.3)

< 1E-06

GSVIVP00022605001

Nicotianamine synthase

1.0 Primary Metabolism

8 (4.7)

7 (0.3)

< 1E-06

GSVIVP00023306001

p-Coumaroyl shikimate 3'-hydroxylase 1

1.9 Secondary Metabolism

8 (4.7)

7 (0.3)

< 1E-06

GSVIVP00002706001

Unknown protein

Unknown

8 (4.7)

7 (0.3)

< 1E-06

GSVIVP00031130001

DNA-damage-repair/toleration (DRT102)

2.4 Replication & Repair

8 (4.7)

8 (0.3)

< 1E-06

GSVIVP00024773001

Acyl-CoA synthetase (Acyl-activating 18)

5.3 Transport System

8 (4.7)

9 (0.4)

< 1E-06

GSVIVP00000809001

Phosphoesterase

Unclear

8 (4.7)

11 (0.4)

< 1E-06

GSVIVP00010326001

Esterase/lipase/thioesterase family

Unclear

8 (4.7)

12 (0.5)

2E-06

GSVIVP00015215001

UDP-glycosyltransferase 85A1

1.0 Primary Metabolism

7 (4.1)

0 (0)

< 1E-06

GSVIVP00026343001

NADPH HC toxin reductase

1.0 Primary Metabolism

7 (4.1)

0 (0)

< 1E-06

GSVIVP00036190001

Catechol O-methyltransferase

1.0 Primary Metabolism

7 (4.1)

0 (0)

< 1E-06

GSVIVP00010293001

F-box domain containing

2.3 Folding, Sorting & Degradation

7 (4.1)

0 (0)

< 1E-06

GSVIVP00025242001

Aspartyl protease

2.3 Folding, Sorting & Degradation

7 (4.1)

0 (0)

< 1E-06

GSVIVP00026388001

Pectinesterase family

4.3 Cell Wall

7 (4.1)

0 (0)

< 1E-06

GSVIVP00015805001

AT-hook DNA-binding protein

Unknown

7 (4.1)

0 (0)

< 1E-06

GSVIVP00008086001

Myb family TF-like b

2.11 Transcription Factors

7 (4.1)

1 (0.1)

< 1E-06

GSVIVP00017803001

Laccase

5.3 Transport System

7 (4.1)

1 (0.1)

< 1E-06

GSVIVP00036529001

Open stomata 1 (OST1)

3.1 Signal Transduction

7 (4.1)

2 (0.1)

< 1E-06

GSVIVP00024338001

Fasciclin arabinogalactan-protein (FLA4)

4.3 Cell Wall

7 (4.1)

2 (0.1)

< 1E-06

GSVIVP00024285001

Zinc transporter (ZIP2)

5.3 Transport System

7 (4.1)

2 (0.1)

< 1E-06

GSVIVP00017555001

UDP-glycosyltransferase 89B2

1.0 Primary Metabolism

7 (4.1)

3 (0.1)

< 1E-06

GSVIVP00018198001

Patatin

8.0 Storage

7 (4.1)

3 (0.1)

< 1E-06

GSVIVP00029089001

Kelch repeat-containing

Unknown

7 (4.1)

3 (0.1)

< 1E-06

GSVIVP00012218001

Myb divaricata

2.11 Transcription Factors

7 (4.1)

4 (0.2)

< 1E-06

GSVIVP00031610001

Unknown protein

Unknown

7 (4.1)

4 (0.2)

< 1E-06

GSVIVP00023356001

alpha-L-Arabinofuranosidase

1.0 Primary Metabolism

7 (4.1)

5 (0.2)

< 1E-06

GSVIVP00028303001

beta-1,3-Glucanase precursor

1.0 Primary Metabolism

7 (4.1)

5 (0.2)

< 1E-06

GSVIVP00030576001

Receptor-like protein kinase

3.1 Signal Transduction

7 (4.1)

5 (0.2)

< 1E-06

GSVIVP00019610001

IAA-amido synthetase GH3.2

3.2 Hormone Signaling

7 (4.1)

5 (0.2)

< 1E-06

GSVIVP00024987001

Allergen Alt a 7

7.0 Stress-related

7 (4.1)

5 (0.2)

< 1E-06

GSVIVP00002843001

Kelch repeat-containing F-box

Unknown

7 (4.1)

5 (0.2)

< 1E-06

GSVIVP00001138001

Flavonoid 3-monooxygenase

1.9 Secondary Metabolism

7 (4.1)

6 (0.3)

< 1E-06

GSVIVP00021523001

Aspartyl protease

2.3 Folding, Sorting & Degradation

7 (4.1)

6 (0.3)

< 1E-06

GSVIVP00023266001

Serine carboxypeptidase K10B2.2

2.3 Folding, Sorting & Degradation

7 (4.1)

8 (0.3)

< 1E-06

GSVIVP00003796001

Glycosyl hydrolase family 1

1.0 Primary Metabolism

6 (3.5)

0 (0)

< 1E-06

GSVIVP00005841001

UDP-glucose glucosyltransferase

1.0 Primary Metabolism

6 (3.5)

0 (0)

< 1E-06

GSVIVP00006924001

Peroxidase

1.0 Primary Metabolism

6 (3.5)

0 (0)

< 1E-06

GSVIVP00023878001

CYP94A1

1.0 Primary Metabolism

6 (3.5)

0 (0)

< 1E-06

GSVIVP00023969001

Class III peroxidase 40

1.0 Primary Metabolism

6 (3.5)

0 (0)

< 1E-06

GSVIVP00037866001

Peroxidase

1.0 Primary Metabolism

6 (3.5)

0 (0)

< 1E-06

GSVIVP00006201001

AP2/ERF114

2.11 Transcription Factors

6 (3.5)

0 (0)

< 1E-06

GSVIVP00033054001

Protein phosphatase 2C

3.1 Signal Transduction

6 (3.5)

0 (0)

< 1E-06

GSVIVP00000122001

Chromosome maintenance MAG2

2.4 Replication & Repair

6 (3.5)

1 (0.1)

< 1E-06

GSVIVP00018988001

Transposon protein

9.0 Transposons

6 (3.5)

1 (0.1)

< 1E-06

GSVIVP00014792001

Carboxylesterase

1.0 Primary Metabolism

6 (3.5)

3 (0.1)

< 1E-06

GSVIVP00033506001

beta-1,3-Glucanase

1.0 Primary Metabolism

6 (3.5)

3 (0.1)

< 1E-06

GSVIVP00014758001

Calmodulin-binding protein AR781

3.1 Signal Transduction

6 (3.5)

3 (0.1)

< 1E-06

GSVIVP00019639001

Peroxidase 73

1.0 Primary Metabolism

6 (3.5)

4 (0.2)

< 1E-06

GSVIVP00009234001

Stilbene synthase

1.9 Secondary Metabolism

6 (3.5)

4 (0.2)

< 1E-06

GSVIVP00020035001

MLK/Raf-related protein kinase 1

3.1 Signal Transduction

6 (3.5)

4 (0.2)

< 1E-06

GSVIVP00025363001

Myb family TF-like a

2.11 Transcription Factors

5 (2.9)

0 (0)

< 1E-06

GSVIVP00026190001

NGA1 TF (NGATHA1)

2.11 Transcription Factors

5 (2.9)

0 (0)

< 1E-06

GSVIVP00037318001

Myb divaricata

2.11 Transcription Factors

5 (2.9)

0 (0)

< 1E-06

GSVIVP00007503001

ACC oxidase homolog 1

3.2 Hormone Signaling

5 (2.9)

0 (0)

< 1E-06

GSVIVP00006975001

Kinesin family member 2/24

4.1 Cell Motility

5 (2.9)

0 (0)

< 1E-06

GSVIVP00021432001

Laccase

5.3 Transport System

5 (2.9)

0 (0)

< 1E-06

GSVIVP00012703001

Aquaporin TIP2;2

5.3 Transport System

5 (2.9)

0 (0)

< 1E-06

GSVIVP00008708001

Monooxygenase (MO3)

1.0 Primary Metabolism

5 (2.9)

0 (0)

< 1E-06

GSVIVP00020827001

AAA-type ATPase

Unclear

5 (2.9)

0 (0)

< 1E-06

GSVIVP00017947001

Unknown protein

Unknown

5 (2.9)

0 (0)

< 1E-06

GSVIVP00021666001

Unknown protein

Unknown

5 (2.9)

0 (0)

< 1E-06

GSVIVP00001266001

Unknown

Unknown

5 (2.9)

0 (0)

< 1E-06

GSVIVP00017730001

CYP77A5P

1.0 Primary Metabolism

5 (2.9)

1 (0.1)

< 1E-06

GSVIVP00006293001

Jasmonate O-methyltransferase

3.2 Hormone Signaling

5 (2.9)

1 (0.1)

< 1E-06

GSVIVP00020849001

ABC transporter B member 11

5.3 Transport System

5 (2.9)

1 (0.1)

< 1E-06

  1. Root-enriched genes were identified by EST frequency comparison of Vitis vinifera roots compared with all other tissues, using the Audic-Claverie (AC) statistic [60]. Gene identifier (ID) from GSVIV, gene description, gene function (from VitisNet annotation), frequency in root and non-root cDNA libraries, and AC confidence statistic are presented. Genes tested for root-enriched expression by real-time qRT-PCR are indicated in bold (Figure 7).
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BMC Plant Biology

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