Table 1.

Overrepresentation of functional categories among the two clusters of differentially expressed genes (see Fig. 5)

		Functional category	Ka	Nb	p valuec
Cluster 1	MIPSd	Protein synthesis	138	511	4.98·10−31
		Ribosomal proteins	95	277	4.29·10−29
		Ribosome biogenesis	106	343	2.46·10−28
		Amino acid metabolism	69	243	3.31·10−15
		Metabolism	221	1530	5.87·10−11
		Metabolism of the aspartate family	26	64	1.75·10−8
		Metabolism of methionine	18	36	3.52·10−7
		Tetracyclic and pentacyclic triterpenes metabolism	16	36	2.84·10−5
		Purine nucleotide/nucleoside/nucleobase metabolism	22	66	4.58·10−5
		Nucleotide/nucleoside/nucleobase metabolism	48	230	4.81·10−5
		Isoprenoid metabolism	16	41	2.55·10−4
		Sulfur metabolism	7	8	3.51·10−4
		Sulfate assimilation	7	8	3.51·10−4
		Metabolism of the cysteine-aromatic group	23	80	4.79·10−4
		Aminoacyl-tRNA-synthetases	15	39	7.46·10−4
		Energy	58	360	1.69·10−2
		Pentose-phosphate pathway	10	24	2.20·10−2
	GOd	Translation	117	345	6.31·10−36
		Cellular amino acid biosynthetic process	44	101	1.10·10−16
		Ribosome biogenesis	46	178	1.13·10−7
		Oxidation reduction	60	270	1.24·10−7
		Metabolic process	76	389	2.49·10−7
		Steroid biosynthetic process	15	24	2.73·10−7
		Sterol biosynthetic process	15	28	5.46·10−6
		Methionine biosynthetic process	16	32	6.13·10−6
		Maturation of SSU-rRNA	22	62	2.28·10−5
		Sulfate assimilation	9	11	3.49·10−5
		rRNA processing	43	195	8.44·10−5
		Methionine metabolic process	10	15	1.36·10−4
		Lipid biosynthetic process	18	52	7.16·10−4
		Ergosterol biosynthetic process	7	9	2.66·10−3
	TFd	FHL1	75	208	1.64·10−24
		RAP1	51	145	1.31·10−15
		SFP1	20	50	1.41·10−6
		GCN4	37	182	8.70·10−4
		HAP1	27	120	2.60·10−3
		MET32	9	24	4.06·10−2
Cluster 2	MIPSd	Unclassified proteins	194	1140	4.13·10−5
		Oxidative stress response	21	56	7.17·10−4
		Cell rescue, defense and virulence	101	558	9.06·10−3
		Degradation of polyamines	5	5	1.98·10−2
		Energy	70	360	2.14·10−2
		Cellular communication	50	239	4.60·10−2
		Cellular signalling	44	202	4.71·10−2
	GOd	Signal transduction	24	74	4.64·10−3
		Protein amino acid phosphorylation	36	141	1.11·10−2
		Proteasomal ubiquitin-dependent protein catabolic process	9	16	3.95·10−2
		Oxidation reduction	56	270	3.96·10−2
		Negative regulation of gluconeogenesis	7	10	4.55·10−2
	TFd	MSN2/MSN4 e	55	166	4.29·10−11
		SKN7	43	175	6.59·10−4
		YAP7	36	152	9.78·10−3
		CAD1	12	32	4.40·10−2

^aNumber of genes present in both the cluster and the functional category

^bTotal number of genes in the functional category

^cA Bonferroni corrected p value cut-off of 0.05 was used and p values indicate the probability of finding the same number of genes in a random set

^dFunctional categories originate from the Munich Information Centre for Protein Sequences (MIPS), Gene Ontology (GO) or transcription factor binding datasets (TF) described in the “Methods” section

^eMSN2/4 transcription factor dataset originates from [30]