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.