TABLE 3.

MIPS functional categories overrepresented among lactic acid-responsive transcripts^a

MIPS category	Significance (log10P value)
	pH 3	Overall pH 5	Common	pH 3	Specific pH 5
Metabolism	(−) 5.26	(−) 10.17	(−) 7.84		(−) 4.15
C compound and CHO metabolism	(−) 5.30	(−) 6.54	(−) 5.09
C compound and CHO utilization	(−) 4.07	(−) 7.17	(−) 3.95		(−) 3.92
C compound and CHO catabolism		(−) 5.18
Amino acid metabolism		(−) 5.97	(−) 3.72
Metabolism of urea		(−) 4.13
N and S utilization		(−) 4.22	(−) 3.78
Energy	(−) 8.30	(−) 6.68	(−) 5.55
Metabolism of energy reserves		(−) 4.54
Transported compounds (substrate)		(+) 3.78/(−) 3.88
Amino acid transport		(−) 4.55	(−) 4.44
Amine/polyamine transport			(+) 3.79
Allantoin/allantoate transport					(−) 4.11
Ion transport		(+) 6.41			(+) 5.23
Cation transport		(+) 5.59			(+) 4.78
Heavy metal ion transport		(+) 9.09			(+) 7.25
Siderophore iron transport		(+) 7.54	(+) 3.99		(+) 3.90
Cell rescue, defense, and virulence		(+) 3.82/(−) 4.17
Ionic homeostasis		(+) 4.35
Homeostasis of cations		(+) 4.64
Homeostasis of metal ions		(+) 8.20			(+) 5.76

^aOverview of MIPS functional categories overrepresented among lactic acid-responsive transcripts identified in a comparison of lactate-challenged and reference anaerobic chemostat cultures of S. cerevisiae CEN.PK 113-7D at pH 3 and pH 5. Overrepresentation is indicated in the upregulated (+) and downregulated (−) gene sets. The overall response includes all genes which responded at each pH, and the common response represents the transcripts which were up- or downregulated at both pH 3 and 5. Values with both + and − indicate significant enrichment of functional categories in both up- and downregulated clusters. The significance of each category is numerically indicated as a log₁₀ P value (as described in Materials and Methods [2]).