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Table 4 Specifically up-regulated transcription factors

From: Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression

RefSeq Accession

Closest Genoscope match

Affymetrix Probeset ID

Young berries

Early-veraison

Late-veraison

Ripe berries

Encoded protein annotation

XM_002282012.2

GSVIVT00014253001

 

125.18

0.51

0.76

0.35

Ethylene-responsive Transcription factor 5

XM_002281930.1

GSVIVT00014247001

 

121.59

1.73

1.03

0.29

Ethylene-responsive Transcription factor 5

XM_002282133.2

GSVIVT00036589001

 

114.34

0.52

0.60

0.45

Ethylene-responsive Transcription factor ERF109

XM_002276536.2

GSVIVT00016398001

1608812_at

105.10

0.15

0.27

0.13

Ethylene-responsive Transcription factor ERF017-like

XM_002282279.1

GSVIVT00023866001

 

90.51

0.24

0.22

0.86

Ethylene-responsive Transcription factor 7-like

XM_002281911.2

GSVIVT00014244001

 

83.05

0.51

0.47

0.14

Ethylene-responsive Transcription factor 5-like

XM_002281777.2

GSVIVT00014237001

1613698_at

80.37

1.36

0.50

0.28

Ethylene-responsive Transcription factor 5

XM_002281895.2

GSVIVT00014242001

1619600_at

73.43

0.80

0.53

0.19

Ethylene-responsive Transcription factor 5

XM_002268377.2

GSVIVT00000349001

 

46.99

0.24

0.15

0.06

Ethylene-responsive Transcription factor WIN1-like

XM_002281047.2

GSVIVT00022870001

1616185_at

39.00

0.11

0.03

0.17

Transcription factor bHLH96-like

XM_002282131.1

GSVIVT00014256001

 

38.48

0.44

0.23

0.13

Ethylene-responsive Transcription factor 5

XM_002280334.1

GSVIVT00032308001

 

36.98

0.00

0.00

0.05

Ethylene-responsive Transcription factor ERF017

XM_002281876.2

GSVIVT00014240001

 

31.92

0.20

0.40

0.10

Ethylene-responsive Transcription factor 5

XM_002281835.2

GSVIVT00014238001

1613799_at

29.46

0.30

0.09

0.00

Ethylene-responsive Transcription factor 5

XM_002284201.1

GSVIVT00014754001

 

29.28

0.35

0.21

0.20

Transcriptional activator Myb

XM_002263558.1

GSVIVT00006679001

 

22.72

0.12

0.00

0.03

Transcription factor RAX1

XM_002263958.2

GSVIVT00008628001

 

19.81

0.04

0.00

0.04

Ethylene-responsive Transcription factor ERF023

XM_002268533.2

GSVIVT00000129001

 

18.68

0.08

0.07

0.16

Transcription factor TCP15-like

XM_002283709.1

GSVIVT00032414001

1609286_at

18.29

0.13

0.05

0.11

GATA Transcription factor 9

XM_002274170.1

GSVIVT00034800001

 

11.10

0.04

0.00

0.03

Transcriptional activator Myb

XM_002276513.1

GSVIVT00037009001

 

9.52

0.08

0.03

0.13

Transcription factor bHLH135

XM_003633976.1

GSVIVT00014248001

 

8.02

0.00

0.09

0.03

Ethylene-responsive Transcription factor 5-like

XM_002283058.1

GSVIVT00020927001

1613614_at

7.56

0.11

0.00

0.00

Transcription factor bHLH135

XM_002276926.1

GSVIVT00029219001

 

7.43

0.00

0.00

0.00

Transcription repressor MYB4

XM_002274226.2

GSVIVT00018597001

 

5.91

0.07

0.00

0.06

Transcription factor bHLH118-like

XM_002284800.1

GSVIVT00014836001

 

5.31

0.07

0.04

0.04

Heat stress Transcription factor B-4

XM_003632349.1

GSVIVT00001240001

1621346_at;

0.10

50.36

25.69

7.32

B3 domain-containing transcription factor ABI3-like

XM_002275111.1

GSVIVT00025350001

 

0.14

30.00

15.82

4.91

Transcription factor HBP-1b(c1)-like

XM_003632364.1

  

0.00

4.66

4.85

0.89

Transcription factor UPBEAT1-like

XM_002283723.2

  

0.00

2.52

0.93

0.06

myb family transcription factor APL-like

XM_002272753.2

GSVIVT00031144001

1609798_at

30.57

50.29

34.79

155.93

Trihelix transcription factor GTL2-like

XM_002276158.2

GSVIVT00017225001

1610832_at

8.91

19.82

17.88

67.73

Probable WRKY transcription factor 32

XM_002281158.1

GSVIVT00028232001

 

5.78

13.73

18.95

61.77

Probable WRKY transcription factor 47-like

XM_003635597.1

 

1611921_at

7.36

16.93

13.95

59.56

GATA transcription factor 26-like

XM_002269660.2

GSVIVT00025898001

 

1.14

9.70

11.70

57.63

WRKY transcription factor 6-like

XM_002273307.2

GSVIVT00013494001

1620116_at

9.62

13.68

10.78

44.93

GATA transcription factor 26

XM_002275540.1

GSVIVT00002773001

1607465_at

1.34

2.26

3.46

43.23

Probable WRKY transcription factor 57

XM_002274248.2

GSVIVT00033300001

 

0.22

0.67

1.28

23.91

Ethylene-responsive transcription factor ERF003

XM_003631122.1

GSVIVT00030611001

1608728_at

6.36

6.37

4.36

19.42

Heat stress transcription factor A-8-like

XM_002267778.1

GSVIVT00006201001

1609629_at

0.76

0.23

0.36

10.56

Ethylene-responsive transcription factor ERF113

XM_002283591.1

GSVIVT00024804001

 

0.10

0.88

1.21

9.53

Ethylene-responsive transcription factor RAP2-11

XM_002275357.2

GSVIVT00003416001

1622116_at

0.59

0.46

0.10

4.36

Transcription factor bHLH144 isoform 2

XM_003632808.1

GSVIVT00034227001

 

0.14

0.88

0.45

4.20

Transcription factor bHLH87-like

XM_002280888.1

 

1618136_at

0.38

0.14

0.16

4.13

Ethylene-responsive transcription factor ERF114-like

XM_002274180.2

GSVIVT00033298001

1609559_at

0.00

0.05

0.19

3.98

Ethylene-responsive transcription factor ERF003 isoform 1

XM_002272053.1

GSVIVT00003403001

 

1.02

0.19

0.23

3.18

Probable WRKY transcription factor 28

XM_002279376.2

GSVIVT00030359001

1618408_at

0.38

0.09

0.06

2.89

Transcription factor bHLH75

XM_002275834.2

GSVIVT00037958001

 

0.59

0.34

0.19

2.80

Ethylene-responsive transcription factor ERF113-like

XM_002285559.1

GSVIVT00015050001

 

0.15

0.53

0.06

2.36

Transcription factor bHLH93

XM_002279450.1

GSVIVT00016545001

 

0.03

0.04

0.02

2.32

Putative transcription factor bHLH041

XM_002284180.2

GSVIVT00025614001

 

0.07

0.08

0.02

1.99

Heat stress transcription factor B-3-like

XM_002264354.2

GSVIVT00007519001

 

0.17

0.00

0.00

1.36

Ethylene-responsive transcription factor ERF098-like

XM_002270623.2

GSVIVT00029005001

 

0.02

0.04

0.02

1.34

Probable WRKY transcription factor 72

XM_002267757.2

GSVIVT00006494001

1607431_at

0.00

0.12

0.00

1.04

Probable WRKY transcription factor 53-like

XM_002279303.1

GSVIVT00020055001

 

0.00

0.00

0.00

0.96

Heat stress transcription factor A-6b

XM_003633801.1

GSVIVT00020889001

 

0.00

0.19

0.17

0.96

AP2-like ethylene-responsive transcription factor AIL5-like

XM_002279882.1

GSVIVT00032269001

 

0.00

0.05

0.00

0.71

Transcription factor WER

XM_002277185.2

GSVIVT00020895001

 

0.05

0.02

0.02

0.68

Probable WRKY transcription factor 72

XM_002274351.1

GSVIVT00037881001

 

0.00

0.00

0.00

0.62

Probable WRKY transcription factor 45

  1. Transcriptions factors that are up-regulated 50-fold or greater in E-L 31 berries, and 3-fold or greater in E-L 35-36 berries or E-L 38 berries. The RPKM values indicating specific up-regulation are shown in bold. Expression values are shown in RPKM for each sample, and fold-changes were calculated relative to a minimum value of 0.1. Matching Genoscope and Probeset IDs are shown if applicable and the putative function of encoded proteins are described by their NCBI annotation. A complete list of all differentially regulated transcripts is presented in Additional file 2.