Table 1.

Gene Ontology categories over-represented in some comparisons between variables

	Rates				Amounts
	GO*	P†	a-P‡	No. of genes§	GO	P	a-P	No. of genes
High correlation
Both low level (4-5)	Cell cycle	<E-17	<0.001	159/370	Cell cycle	<E-7	0.001	112/300
	Meiosis	<E -6	0.003	52/122	-
	Regulation of physiological process	<E-16	<0.001	204/518	Regulation of physiological process	<E-10	<0.001	171/459
	DNA binding	<E -12	<0.001	88/190	DNA binding	<E -8	<0.001	66/146
	Protein kinase activity	<E -13	<0.001	64/117	-
	DNA metabolism	<E -11	<0.001	158/422	DNA metabolism	<E -5	0.017	39/372
	Response to endogenous stimulus	<E -6	0.004	65/164	-
	Regulation of transcription	<E -10	<0.001	120/298	Regulation of transcription	<E -6	0.001	99/263
	-				RNA splicing	<E -6	0.002	47/103
	Lipid kinase activity	<E -5	0.005	8/8	-
Both high level (1-2)	Cytosolic ribosome	<E -24	<0.001	93/147	Cytosolic ribosome	<E -78	<0.001	149/156
	Protein biosynthesis	<E -15	<0.001	179/439	Protein biosynthesis	<E -48	<0.001	247/417
	Hydrogen ion transporter activity	<E -6	0.001	25/43	Hydrogen ion transporter activity	<E -11	<0.001	33/43
	-				Carboxylic acid metabolism	<E -18	<0.001	134/258
	Mitochondrial matrix	<E -7	0.001	64/150	-
	Redox activity	<E -8	<0.001	93/228	Redox activity	<E -17	<0.001	107/197
	Mitochondrial ribosome	<E -5	0.01	36/78	-
	-				Ribosome biogenesis	<E -14	<0.001	97/182
	Proteasome complex	<E -8	<0.001	28/43	Proteasome complex	<E -13	<0.001	36/45
	Nucleotide metabolism	<E -5	0.044	35/79	Nucleotide metabolism	<E -11	<0.001	49/79
	Endoplasmic reticulum	<E -7	0.001	127/356	Endoplasmic reticulum	<E -07	<0.001	118/290
	Hexose catabolism	<E -5	0.007	17/26	Hexose catabolism	<E -06	0.005	18/26
	Protein folding	<E -6	0.001	33/62	-
	-				Cell wall	<E -6	0.001	29/50
Low correlation
Low level in RNA (4/5), high in protein (1/2)	Ribosome biogenesis	<E -5	0.022	24/190
	Spore wall assembly	<E -6	0.006	10/35
	Glycoprotein biosynthesis	<E -5	0.01	13/66
	Oxidoreductase activity, acting on the CH-CH group	<E -5	0.019	5/9
	Protein amino acid glycosylation	<E -5	0.046	12/62
Low level in protein (4/5), high in RNA (1/2)	-				Membrane	< E -6	0.001	46/665
	-				Transporter activity	< E -6	0.001	24/246
	-				Cell wall	< E -6	0.002	10/50
	-				Vacuole	< E -5	0.012	15/128

*Comparisons were done as in Figure 2. Then, the genes corresponding to different levels of correlation were divided into groups according to their expression level and the GOs were searched. Only statistically significant categories are shown. High correlation class includes both very high and high correlation classes from Figure 2b, while the low correlations include both low and very low correlations classes, also from Figure 2b. ^†Absolute p value. ^‡Adjusted p value. ^§The number of genes shows how many of the genes in the GO category present among the genes analyzed in each pairwise comparison are within the selected quintile.