Table 3. Transcripts that require both Msa1 and Msa2 for full repression.

gene	MBF/SBF	peak	description	msa1/WT	msa2/WT	msa1msa2/WT
THI44,7			thiamine synthesis; required for mt genome stability in response to DNA damage	0.18	-0.14	1.77
MAM15			Monopolin; kinetochore protein; chromosome attachment to meiotic spindle	0.16	0.06	1.75
YFL012W			unknown function; null mutant increases resistance to rapamycin	0.42	0.32	1.50
FUR17			synthesizes UMP from uracil; involved in the pyrimidine salvage pathway	0.30	0.32	1.27
YLR162W			unknown function; overexpression causes growth arrest and apoptosis	-0.58	0.11	1.23
URA27			first two enzymatic steps in pyrimidine biosynthesis; feedback inhibited by UTP	0.38	0.12	1.23
TIR14,6		52	Cell wall protein; downregulated in acid, induced by cold shock and anaerobiosis	0.03	-0.12	1.18
FUI1			uridine permease; moves to the vacuole upon DNA replication stress	0.42	0.54	1.17
CRS5			Copper-binding metallothionein; required for wild-type copper resistance	0.54	0.56	1.17
YLR194C		5	cell wall protein; expression is upregulated in response to cell wall stress	0.56	0.29	1.01
STE3			a factor receptor; mediates pheromone response; required for mating	0.21	-0.41	0.95
RPS22B			Protein component of the small (40S) ribosomal subunit	0.45	0.37	0.92
ACA1			ATF/CREB transcription factor; important for carbon source utilization	0.31	0.51	0.89
DAN14,6			Cell wall mannoprotein; expressed only under anaerobic conditions	0.25	-0.52	0.86
IRC7			Beta-lyase involved in thiol production; null mutant increases Rad52p foci	-0.31	-0.47	0.84
SFG1		66	transcription factor; required for growth of pseudohyphae	0.59	-0.17	0.84
FDH1			NAD(+)-dependent formate dehydrogenase	-0.35	-0.18	0.83
RPL9B			Ribosomal 60S subunit protein L9B	0.30	0.04	0.81
AFT14,5			Transcription factor for iron deficiency; nuclear upon DNA replication stress	0.24	0.32	0.81
HSP314			stress, diauxic shift, and stationary phase survival; up in DNA replication stress	0.24	0.36	0.80
MEK15			Meiosis-specific protein kinase; meiotic checkpoint and recombination	0.42	0.32	0.80
ECM12			unknown function; mutants display zymolyase hypersensitivity	0.22	0.44	0.77
YKE4			Zinc transporter in the ER; null mutant leads to zinc accumulation in cytosol	0.26	0.38	0.76
SNA2			unknown function; has similarity to Pmp3p, which is involved in cation transport	-0.12	0.47	0.76
YJL213W			unknown function that may interact with ribosomes	0.05	-0.04	0.75
TIR34,6		65	Cell wall mannoprotein; required for anaerobic growth	0.60	0.26	0.74
SMF3			metal transporter involved in iron homeostasis; increases in DNA replication stress	0.38	0.52	0.73
DAL4			Allantoin permease; expression sensitive to nitrogen catabolite repression	0.01	0.36	0.73
TIR44,6			Cell wall mannoprotein; required for anaerobic growth; induced by cold shock	0.04	0.09	0.71
SPR285			Sporulation-specific homolog of the Cdc3/10/11/12 family of septins	0.03	0.14	0.71

Columns as reported in Table 2. Gene ontology terms are superscripted as:

⁴ response to stress,

⁵ meiotic cell cycle,

⁶ cell wall protein family,

⁷ pyrimidine biosynthesis.