Table 1 a

Technology	Reference	URL (http://…)	# ORFs covered	Description	
Gene chip	Holstege, Jennings et al. 1998 (9)	web.wi.mit.edu/young/ expression	5455	Vegetative growth	
	Jelinsky and Samson 1999 (11)	www.hsph.harvard.edu/ geneexpression	6281	Response to alkylating agent	
	Roth, Hughes et al. 1998 (10)	arep.med.harvard.edu/ mrnadata/expression.html	6214	Mat. type a, glucose (30 deg. C)	
				Mat. type a, glucose (30 deg. C)	
				Mat. type a, galactose (30 deg. C)	
				Mat. type a, glucose (39 deg. C)	
Serial Analysis of Gene Expression (SAGE)	Velculescu, Zhang et al. 1997 (1)	www.sagenet.org/ yeast/yeastintro.htm	3005	Yeast transcriptome – G2/M phase	
				Log phase	
				S phase	
cDNA microarray	DeRisi, Iyer et al. 1997 (5)	cmgm.stanford.edu/ pbrown/explore	6153	Time course of diauxic shift	

Table 1 b

Feature			G(F)			T(F)	D(F)	
Amino acids, in particular Ala	Number of Ala in yeast genome	Number of amino acids in yeast	Genome composition of Ala in yeast	Number of Ala weighted by expression	Number of amino acids weighted by expression	Transcriptome composition of Ala in yeast	Relative enrichment of Ala in transcriptome	
Numbers	141890	2574876	5.5%	347801	4758441	7.3%	32.7%	
Folds, in particular the TIM-barrel (3.1)	Number of TIM-barrel fold matches in yeast genome 	Number of matches with all folds in yeast genome	Genome composition of TIM-barrel fold matches	Number of TIM-barrel fold matches weighted by expression	Number of matches with all folds weighted by expression	Transcriptome composition of TIM-barrel fold matches	Enrichment of TIM-barrel fold matches in transcriptome	
Numbers	65	1560	4.2%	389	4709	8.3%	97.8%