Table 2

New candidate Zap1 target genes identified by E1, E2, and E3 clustering.

ORFa

Gene

Function

Fold induction

ZRE



E1b

E2b

E3-1c

E3-2c

startd

scoree

sequencef


YBL029W

function unknown

3.0

2.9

1.6

1.4

-995

5.8

CCCCTGCCGGT

YBR072W*

HSP26*

small heat shock protein, protein folding

40.5

2.0

3.3

3.5

-451

5.3

ACCTTGCCTGT

YDR077W*

SED1*

cell wall protein

2.6

2.2

2.6

2.1

-896

4.7

CCCTTATAGGA

YGR088W*

CTT1*

catalase T, oxidative stress resistance

17.1

3.7

1.9

1.7

-337

5.7

CCCTTACCGGT

YGR243W

FMP43

mitochondrial protein, function unknown

2.8

2.7

3.1

2.5

-552

4.9

TCCTCGAATGT

YHR214W-A

function unknown

6.5

2.6

3.0

3.2

-274

4.8

ACCTCTGGTGT

YIL045W

PIG2

putative protein phosphatase regulatory subunit

4.6

2.4

1.6

1.5

-859

4.7

ACCTTCCACGT

YJL048C*

UBX6*

UBX (ubiquitin regulatory X) domain-containing protein

2.3

3.3

1.8

1.6

-198

5.2

TCCATTAAGGT

-39

5.9

CCCTCAAAGGA

YKR046C

PET10

lipid particle protein, unknown function

2.9

3.0

1.7

1.7

-929

4.8

ATCTTGCAGGT

YLR136C*

TIS11*

tristetraproline homolog, control of mRNA stability

2.6

4.1

5.6

3.7

-821

4.9

GCCCGTGAGGT

-768

6.3

AACCTGCGGGT

-507

6.0

GCCCAGAGGGT

YML028W

TSA1

peroxiredoxin, oxidative stress resistance

5.0

2.9

2.0

1.5

-195

5.5

GCCCGTCGGGT

-170

7.2

TCCCTAAAGGA

YMR181C

function unknown

5.9

2.2

2.6

2.7

-237

5.1

CCCTTCGAGGG

YNL239W*

LAP3*

homocysteine thiolactonase

2.1

4.7

2.9

2.9

-947

4.8

GCCTCCAATGT

YOL082W

ATG19

autophagy and cytoplasm-to-vacuole (CVT) targeting pathway

4.3

3.2

1.6

1.4

-281

5.9

ACCTTAAAAGT

-998

4.9

ACCAACAGGGT

YOL155C*

cell wall protein

11.8

3.5

2.3

2.9

-361

6.3

ACCGTGCAGGA

YPL159C

PET20

mitochondrial protein required for respiratory growth

9.1

5.2

4.5

4.0

-278

5.3

GCCATTAAGGT

-180

5.6

ACCCTTTGGGA


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.

f) 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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