Table 3

New candidate Zap1 target genes identified by E3 and E4 clustering.

ORFa

Gene

Function

Fold inductionb

ZRE



E3-1

E3-2

E4-1

E4-2

startc

scored

sequencee


YDL125C*

HNT1*

adenosine 5'-monophosphoramidase

1.9

1.6

3.6

4.1

-279

6.9

GCCTCAAAGGT

YEL060C*

PRB1*

vacuolar proteinase B

2.6

2.8

2.0

2.1

-677

6.5

GCCATGAGGGT

YFL014W

HSP12

cell wall protein, stress resistance

1.5

1.5

4.4

3.7

-211

5.0

ACCTCAAAGTT

YGR254W

ENO1

enolase I, glycolysis and gluconeogenesis

2.6

2.9

1.4

1.7

-927

9.4

ACCGTGAAGGT

-371

5.1

ACCTGAGCGGT

-216

5.6

CACCTCAAGGT

YGR279C*

SCW4*

cell wall protein with similarity to glucanases

1.8

1.9

1.5

1.4

-481

5.4

CCCTGCACGGT

-466

6.3

ACCCTCTGGGA

YHR174W*

ENO2*

enolase II, glycolysis and gluconeogenesis

2.5

2.8

1.3

1.6

-594

4.8

ACGCTGCGGGT

YIL169C*

cell wall potein

3.4

3.1

2.1

2.2

-742

10.8

ACCCGGAAGGT

-252

6.0

ACCTCGCAGGC

YJL052W

TDH1

glyceraldehyde-3-phosphate dehydrogenase

1.4

1.6

1.6

1.6

-347

4.6

ACCTTCGGAGT

YJL171C

cell wall protein

1.6

1.8

1.6

1.8

-573

4.9

CCCATAAAGGA

YKR042W*

UTH1*

mitochondrial protein, oxidative stress resistance

3.5

4.0

1.4

1.5

-282

6.9

CCCTTCAATGT

YLL053C

aquaporin

1.6

1.5

1.7

1.5

-354

5.5

ACCGGTCGGGT

YMR169C

ALD3

aldehyde dehydrogenase

2.0

1.9

1.6

1.5

-214

9.1

TCCCTAAGGGT

-79

4.6

ACCTGGCATGA

YOR348C

PUT4

proline permease

1.8

1.8

1.9

1.8

-299

8.2

CCCTGCAAGGT

YPL274W*

SAM3*

S-adenosylmethionine permease

1.9

1.7

2.1

2.2

-240

4.7

TCCCCTGCGGT

YPR003C

putative ER sulfate permease

2.2

2.1

1.5

1.5

-149

5.5

ACCGAAAAGGT


a) Results for genes marked with asterisks were confirmed independently by S1 nuclease protection assay in Figure 2.

b) Results from two independent microarray experiments (E3-1, E3-2; E4-1, E4-2) for each condition are shown.

c) Numbers indicate the distance from the ATG initiation codon.

d) Score calculated for each sequence with a position-specific scoring matrix generated by RSAT.

e) ZREs shown in bold were tested for interaction with Zap1 as described in Figure 3A.

Wu et al. BMC Genomics 2008 9:370   doi:10.1186/1471-2164-9-370

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