Table 1

Confirmation of previously identified Zap1 target genes by E1, E2, and E3 clustering.

ORFa

Gene

Function

Fold induction

ZRE



E1b

E2b

E3-1c

E3-2c

startd

scoree

sequence


Experimentally tested Zap1 target genes


YDR284C

DPP1

diacylglycerol pyrophosphate phosphatase

5.5

3.6

2.4

2.2

-452

9.6

ACCTGAAAGGT

YDR492W

IZH1

membrane steroid hormone receptor ortholog

2.8

4.4

1.4

1.6

-914

5.0

TCCCTCAATGA

-417

11.2

ACCCTAAAGGT

YGL255W

ZRT1

plasma membrane zinc uptake transporter

24.2

18.9

38.8

34.4

-456

9.3

ACCTTTGGGGT

-338

7.7

ACCTCGAAGGA

-319

12.0

ACCTTGAGGGT

-204

11.7

ACCTTGAAGGT

YGL256W

ADH4

alcohol dehydrogenase IV

26.2

5.6

12.6

12.6

-269

9.4

ACCGTGAAGGT

-191

5.3

GCCTTCAATGA

YJL056C

ZAP1

zinc-responsive transcriptional activator protein

7.5

16.9

96.5

79.7

-144

11.2

ACCCTAAAGGT

YKL175W

ZRT3

vacuolar zinc export transporter

7.9

8.7

4.9

4.8

-155

11.6

ACCTTAAGGGT

YLR130C

ZRT2

plasma membrane zinc uptake transporter

5.6

12.3

2.7

2.5

-941

6.1

ACCCTAACTGT

-311

11.2

ACCCTAAAGGT

-262

11.2

ACCCTAAAGGT

-174

5.8

ACCTTTTGGGA

-112

4.9

ACCAACAGGGT

-41

5.3

GCCTGCAATGT

YMR243C

ZRC1

vacuolar zinc import transporter

2.1

4.7

1.6

1.8

-174

9.6

GCCTTGAAGGT

YMR319C

FET4

plasma membrane Fe/Cu/Zn uptake transporter

2.3

2.4

1.6

1.7

-384

7.8

ACCCCACGGGT

YNR039C

ZRG17

endoplasmic reticulum zinc import transporter

3.2

3.5

2.3

1.9

-527

11.7

ACCTTGAAGGT

YOL002C

IZH2

membrane steroid hormone receptor ortholog

1.9

2.0

3.4

3.3

-256

7.7

ACCCTAGAGGA

-173

7.2

ACCCCGAGTGT

YOL154W

ZPS1

cell wall protein, putative metalloprotease

13.9

10.1

78.6

57.9

-329

11.8

ACCTTCAGGGT

-314

11.8

ACCTTCAGGGT


Likely Zap1 target genes


YBL049W

MOH1

zinc-binding protein, function unknown

10.7

2.2

3.2

3.8

-387

8.7

CCCTTGAGGGA

YBR117C*

TKL2*

transketolase, pentose phosphate pathway

5.4

2.0

1.9

2.1

-844

8.2

ACCTTATGGGT

-524

5.3

ACCCAAAATGT

YDR055W*

PST1*

cell wall protein

5.0

2.7

2.0

1.9

-886

7.4

ACCCCAAGGGA

-405

8.0

TCCTTGAGGGA

YGL121C

GPG1

putative gamma subunit of a heterotrimeric G protein

10.8

2.7

2.1

2.4

-287

8.3

CCCTTCGAGGT

-208

9.0

ACCGTAAAGGT

YGL257C

MNT2

mannosyltransferase, O-linked glycosylation

2.3

4.4

4.0

3.7

-572

5.3

GCCTTCAATGA

-494

9.4

ACCGTGAAGGT

YGL258W

VEL1

function unknown

16.3

4.0

112.6

78.6

-763

6.3

ACCTTGCATGA

-232

10.4

ACCCTGCGGGT

YGR295C

COS6

function unknown

2.7

2.2

1.5

1.6

-875

5.0

AACTTAAATGT

-309

9.1

ACCTTAAATGT

YJL132W*

similar to phospholipase D

5.2

3.8

3.3

2.8

-154

7.8

ACCCAAAGGGT

YJR061W

Mnn4-related, N-linked glycosylation

4.6

2.1

2.0

1.8

-278

9.8

ACCTTCAAGGA

YKL165C

MCD4

glycosylphosphatidylinositol (GPI) anchor synthesis

4.1

2.5

1.8

1.8

-104

11.4

ACCTTAAAGGT

YLL020C

function unknown

5.1

3.1

1.7

1.6

-933

12.0

ACCTTGAGGGT

YMR120C

ADE17

AICAR transformylase, purine biosynthesis

5.2

3.7

1.9

2.2

-98

8.7

ACCTTTAGTGT

YMR271C

URA10

orotate phosphoribosyltransferase, pyrimidine biosynthesis

6.1

2.5

4.9

5.2

-143

7.9

ACCTTTCGGGA

YMR297W

PRC1

vacuolar carboxypeptidase Y

3.0

3.5

1.5

1.9

-182

8.1

ACCCCGCGGGT

YNL254C

function unknown

9.7

12.0

2.3

2.0

-432

11.7

ACCTTGAAGGT

YNL336W

COS1

function unknown

2.1

2.0

1.6

1.6

-871

5.0

AACTTAAATGT

-591

5.3

AACCTAGAGGT

-314

9.1

ACCTTAAATGT

YOL084W

PHM7

major facilitator superfamily member, function unknown

9.7

2.1

2.5

2.3

-766

11.7

ACCTTGAAGGT

YOL131W

function unknown

5.0

2.3

2.5

2.2

-1000

7.6

AACTTCAGGGT

-458

8.2

ACCTGGAAGGA

-364

5.9

ACCCAAGAGGT

-122

5.5

TCCATTAGGGT

YOR387C

function unknown

17.8

19.3

136.4

113.6

-763

6.3

ACCTTGCATGA

-231

10.4

ACCCTGCGGGT

YOR134W

BAG7

GTPase-activating protein, control of cell wall synthesis

5.9

2.0

1.7

1.6

-445

6.0

CCCTCCAAGGA

-325

8.6

CCCCTGCAGGT

YPL250C*

ICY2*

function unknown

2.1

2.3

3.1

3.1

-756

8.9

CCCTTCCGGGT

-524

7.4

ACCCCAAGGGA

-475

5.7

GCCCAAAGGGT

-360

5.6

CCCGTCAGTGT


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

b) Expression ratios are the average of two independent microarray experiments (Lyons et. al. 2000).

c) Results from two independent microarray experiments (E3-1 and E3-2) are shown.

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

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

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

Open Data