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Table 1.

Yeast RNA Expression Data Sets Incorporated into Data Analysis

Ref[ii]	Method[iii]	Series code[iv]	Raw data series obtained	Norm.series produced	Data codes[v]	Experimental preparations[vi]	Microarray control preparations[vi]	Remarks
1	S	Vel	3	3		YPH499 (MAT a) in YPD rich medium at 30°C as above + 100 mm hydroxyurea as above + 15 μg/ml nocodazole	N/A	early log phase G₁/S arrest G₂/M arrest
2	M	Der_diaux	14	8	T,I	DBY7286 (MAT a) in YPD at 30°C	initial time point	diauxic shift
		Der_tup	2	2	C	TUP1Δ (TUP1::LEU2) in rich medium + glucose	wild-type strain
		Der_yap	2	2	C	YAP1++ (plasmid,GAL1-10 promoter) in galactose	wild-type strain + control plasmid
3	M	Chu_spo	14	8	T,I	YSC328 (MAT a/α) in sporulation inducing medium	initial time point	sporulation
		Chu_ndt80_del	4	3	T,I	YSC330 (MAT a/α ndt80::LEU2) in sporulation inducing medium	initial time point	sporulation mutant
		Chu_gal_ndt80	2	2	C	YSC553 (MAT a GAL1-10 promoter::NDT80) in galactose	GAL1-10 promoter::URA3strain	sporulation control mutant
4	A	Cho	17	17		K3445 (cdc28-13), K2994 (cdc15-2) synchronized at 37°C and then grown at 25°C	N.A.	synchronized cell culture
5	A	Rot	4	4		FY4 (MAT a) in 2% glucose at 30°C	N.A.	glucose
						as above, then 39°C heat shock		heat shock
						as above in 2% galactose at 30°C		galactose
						FY5 (MATα) in 2% glucose at 30°C		mating type
6	A	Hol	42	42		strains:	N.A.	comparison of RNA
						• 11 experimental strains with mutant RNA polymerase subunit genes • 8 control strains with wild-type RNA polymerase subunit genes		polymerase subunit mutants with isogenic wild type strains grown under identical conditions.
						conditions:
						YPD at 30°C to mid-log phase. For ts mutant/wild-type pairs, heat shock at restrictive temperature for 45 min before assaying		all experiments replicated and replicated data reported except for KIN28
7	M	Spe_alpha	36	36	T,D	DBY8724 (MAT a) cell cycle synchronized by α factor which is then removed centrifugally	asynchronous culture	synchronized cell cultures
		Spe_elut	28	28	T,D	DBY7286 (MAT a) cell cycle synchronized by elutriation	asynchronous culture
		Spe_cdc15	48	46[vii]	T,D	DBY8728 (MATα cdc15-2^ts ) cell cycle synchronized by temperature manipulation	asynchronous culture
		Spe_cln3	4	3	T,I	DBY8725 (MAT a cln1::HIS3 cln2::TRP1 cdc34-2^tsura3-GAL–CLN3) at restrictive temperature in galactose	no galactose, entire control culture harvested at time 0	experimental performed twice
		Spe_clb2	4	3	T,I	DBY8726 (MAT a clb1::URA3 clb2::LEU2 clb3::TRP1 clb4::HIS3 GAL–CLB2) in DMSO and nocodazole in galactose	no galactose, entire control culture harvested at time 0	experiment performed twice
		Spe_wtgal	2	2	C	DBY8727 (MAT a) in galactose	no galactose	control forcln3, clb2sets
8	M	Mye	4	4	C	MG107 (MAT a med2Δ1::TRP1) in galactose, under heat shock	MG106 (MAT a MED2) under same conditions	mediator complex
9	A	Coh	4	4		Yap1 vs. wild type, with and without peroxide		oxidative stress
		TOTAL	234	217

[i] Information provided includes the literature reference and corresponding web site, method used to assay RNA (Method), the number of raw data series obtained through public access or personal communication from the reference, number of normalized data series generated using methods described in the text, and summaries of strains and conditions used. Note that data obtained may only represent a selection of the total data collected and discussed by the reference, as some data may not have been reported. ExpressDB database also contains data from Eisen et al. (1998) and Marton et al. (1998).

[ii] Reference for sets of experiments considered by this study and associated web site, where available. (1) Velculescu et al. (1997),ftp://genome-ftp.stanford.edu/pub/yeast/tables/SAGE_Data/; (2) DeRisi et al. (1997), http://cmgm.stanford.edu/pbrown/explore/index.html; (3)Chu et al. (1998),http://cmgm.stanford.edu/pbrown/sporulation/index.html; (4) Cho et al. (1998), http://genomics.stanford.edu/yeast/full_data.html; (5) Roth et al. (1998), http://arep.med.harvard.edu; (6) Holstege et al. (1998),http://www.wi.mit.edu/young/expression.html; (7) Spellman et al. (1998), http://genome-www.stanford.edu/cellcycle; (8) Myers et al. (1999), http://cmgm.stanford.edu/pbrown/med2; (9) B. Cohen, (unpubl.).

[iii] (S) SAGE (Velculescu et al. 1995); (M) DNA microarray (DeRisi et al. 1997); (A) Affymetrix oligonucleotide array (Lockhart et al. 1996; Wodicka et al. 1997)

[iv] Abbreviation used in text for a set of related experiments. Series codes are based on the first three letters of the primary author name of the source data literature reference.

[v] Properties of the data series and their handling: (C) A single control preparation (see below) described in the Microarray control preparation column is used with every experimental preparation. This control preparation is not an initial time point of a time series of experimental measurements. (D) Different control preparations are used with every experimental preparation for a microarray-based series of experimental measurements. (I) A single control preparation is used with every experimental preparation. This control preparation is an initial time point of a time series of experimental measurements. (T) Experimental preparations are a time series of a single culture growing under defined conditions. Microarray control data series coded as C and I are aggregated and their corresponding experimental measurements are calibrated as part of the procedure for computing microarray-derived estimated relative abundances described on our web site.

[vi] Preparation is here defined as a sample of a culture of a defined yeast strain grown under defined environmental conditions for a defined period of time that has been extracted for purposes of an RNA expression level assay. Strains and conditions are described under Experimental preparations for every set of experiments except for Hol (see the web site associated with the reference for Hol). When using microarrays, measurements of RNA levels for experimental preparations are gathered with measurements of RNA levels for a control preparation which is described under Microarray control preparations. Only relevant differences from the experimental preparation are described in the control preparation column. In these two columns details of the medium and genotype are omitted unless they are central to the experiment, e.g., common auxotrophic mutations such as ura3-52, lys2-801, ade2-101, leu2-Δ1, his3-Δ200, and trp1-Δ63along with corresponding amino acid supplements to media are omitted. (N.A.) Not applicable.

[vii] Two series reported for time points 120 and 160. The second series was used in each case in preference to the first for computing the microarray-derived estimated relative abundances described on our web site.