TABLE 3.

Enrichment of transcription factor motifs (TFMs) and MIPS functional categories in clusters of genes that were differentially expressed in response to anaerobiosis in glucose medium (wild-type strain, SOM clustering with 1D ring topology)^a

Cluster no.	n	TFM	Reference(s)	Percentage share	P		MIPS functional category	P (genomic)
					In set	Genomic
1	20	MSN2/4	46	95	5.3	8.0	Metabolism of energy reserves (glycogen, trehalose)	11.0
		MIG1	46	50	3.7	4.5	C-compound and carbohydrate metabolism	5.7
2	16	MSN2/4	46	88	3.1	5.0	Cell rescue, defense, and virulence	4.4
3	16	ABF1	91	63	2.0	2.1	Respiration/mitochondrion/energy	≥3.5
							Transport ATPases	3.8
4	34	HAP2/3/4/5	46	44	3.0	4.8	Respiration/mitochondrion/energy	≥8.7
		HAP1	48	26	2.3	4.9
5	40	PDR1	54	13	2.4	3.9	Respiration/mitochondrion	≥2.7
							Homeostasis of cations	2.2
6	75						Mitochondrion	14.0
							Ribosome biogenesis	8.5
							Phosphate metabolism	2.2
7	10	ACE2	54, 91	70	3.0	3.2	C-compound and carbohydrate metabolism	3.6
		NDD1	54	50	2.8	3.4
		SWI4	54	50	2.6	3.0
8	42	ROX1	17	95	2.7	4.0	Vitamin, cofactor, and prosthetic group biosynthesis	2.1
		HAP2/3/4/5	54	62	2.6	2.8
9	34	UPC2	16	76	7.9	12.7	ABC transporters	3.4
							Cell rescue, defense, and virulence	3.2
10	38	MCM1	46, 76, 91	82	3.6	5.2	Cell wall	5.6
		GLN3	91	71	2.1	2.3	Cell rescue, defense, and virulence	3.7
		UPC2	16	63	4.8	9.0	C-compound and carbohydrate utilization	2.4
11	20
0	7						Mitochondrion	2.2

^aSee Table 1, footnotes a to d.