Table 2 Enrichment of transcription factors (TF) binding in clusters of genes that were differentially expressed in response to fully fermentative conditions. Clusters A & B, 2 & 3 and 4, 5 & 6 had similar expression pattern and similar enrichments, thereby these were analyzed together. Enrichment of TF binding according to the dataset of Harbison et al. [57] was given in p-value. Specific TF binding sites not present in the Harbison dataset (PAC, RRPE and Upc2p) were analyzed by using web-based software RSAT http://rsat.ulb.ac.be/rsat/ and indicated in italics.

B

AAACTGTGG

22

6

2.94E-04

NC

TGAsTCA

192

22

3.54E-05

20

2.54E-05

NC

TGACTC

36

14

1.19E-11

NC

CAyCCrTrCA

157

49

2.79E-33

NC

AyCCrTACAy

51

25

5.25E-23

NC

TGTAyGGrTG

203

72

3.54E-54

NC

GATAAGa

92

7

2.35E-04

-

wGmGATGAGv [22]

376

98

5.7

-

TGAAAAwTTT [22]

535

110

4.2

NC

TCGTwhAG [42]

667

16

1.7

Transcription factor

1

2&3

4,5&6

cluster^a

binding motif

nr of genes^b

nr of genes^c

p-value

nr of genes^c

p-value

nr of genes^c

enrichment^d

NC

GGaCCCT

128

25

1.59E-04

NC

GGnnATAnCGs

73

25

1.75E-09

5

mAGGGGsGG

65

20

5.57E-07

A

GCsGsGnnsG

50

17

8.21E-07

NC

GnCnnGsCs

156

37

2.56E-08

5

mAGGGG

56

18

1.00E-06

NC

TTCynnnnnnTTC

133

31

5.38E-07

3

GnCcAAtcA

54

16

1.31E-05

NC

yTGACT

20

7

1.29E-03

NC

TGCAGnnA

79

20

1.55E-05

NC

TAGCCGCCsA

132

28

1.33E-05

3

GGTGGCAAA

93

21

1.60E-04

NC

ACGCGT

165

44

1.75E-10

NC

CGCGAAAA

140

27

3.32E-04