Brief Description	# of Conditions	Full Description	First Author	All Authors	Publication Title	Journal	Year	PubMed ID
rsc3/rsc30 knockouts	8	DNA microarray analysis with rsc3 or rsc30 mutants reveals different effects on the expression levels of ribosomal protein genes and cell wall genes	Angus-Hill ML	"Angus-Hill ML, Schlichter A, Roberts D, Erdjument-Bromage H, Tempst P, Cairns BR"	A Rsc3/Rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler RSC in gene expression and cell cycle control.	Mol Cell	2001	11336698
slt2/swi4/swi6/bck1 knockouts	5	Transcriptional coregulation by the cell integrity mitogen-activated protein kinase Slt2 and the cell cycle regulator Swi4	Baetz K	"Baetz K, Moffat J, Haynes J, Chang M, Andrews B"	Transcriptional coregulation by the cell integrity mitogen-activated protein kinase Slt2 and the cell cycle regulator Swi4.	Mol Cell Biol	2001	11533240
splitomicin exposure and sir2 mutants	7	Identification of a small molecule inhibitor of Sir2p	Bedalov A	"Bedalov A, Gatbonton T, Irvine WP, Gottschling DE, Simon JA"	Identification of a small molecule inhibitor of Sir2p.	Proc Natl Acad Sci U S A	2001	11752457
Oxidative stress and glutaredoxin 5-deficient mutant	9	"Transcriptome analysis of glutaredoxin 5-deficient (grx5) mutant, a model for continuous moderate oxidative stress. Respiratory petite (pet117) mutants and wild type also examined."	Belli G	"Belli G, Molina MM, Garcia-Martinez J, Perez-Ortin JE, Herrero E"	Saccharomyces cerevisiae glutaredoxin 5-deficient cells subjected to continuous oxidizing conditions are affected in the expression of specific sets of genes.	J Biol Chem	2004	14722110
Histone deacetylase (rpd3/sin3/hda1 deletions)	6	"Here, we present transcription profiles of the yeast deletion strains rpd3, sin3, sap30, ume6, hda1, hos2, and hos3. In addition, we present profiles of wild-type yeast treated with TSA in concentration- and time-dependent manners"	Bernstein BE	"Bernstein BE, Tong JK, Schreiber SL"	Genomewide studies of histone deacetylase function in yeast.	Proc Natl Acad Sci U S A	2000	11095743
Histone deacetylase (sin3/sap30/ume6/hda1/hos2/hos3 deletions)	7	"Here, we present transcription profiles of the yeast deletion strains rpd3, sin3, sap30, ume6, hda1, hos2, and hos3. In addition, we present profiles of wild-type yeast treated with TSA in concentration- and time-dependent manners"	Bernstein BE	"Bernstein BE, Tong JK, Schreiber SL"	Genomewide studies of histone deacetylase function in yeast.	Proc Natl Acad Sci U S A	2000	11095743
Trichostatin A treatment time course	5	"Here, we present transcription profiles of the yeast deletion strains rpd3, sin3, sap30, ume6, hda1, hos2, and hos3. In addition, we present profiles of wild-type yeast treated with TSA in concentration- and time-dependent manners"	Bernstein BE	"Bernstein BE, Tong JK, Schreiber SL"	Genomewide studies of histone deacetylase function in yeast.	Proc Natl Acad Sci U S A	2000	11095743
leu3 mutant expression profiles	12	Analysis of leu3 mutant grown in either limited ethanol or limited ammonium media. Leu3p regulates a gene involved in nitrogen assimilation and six genes involved in branched chain amino acid metabolism. Results provide insight into the role of Leu3p in gene regulation.	Boer VM	"Boer VM, Daran JM, Almering MJ, de Winde JH, Pronk JT"	Contribution of the Saccharomyces cerevisiae transcriptional regulator Leu3p to physiology and gene expression in nitrogen- and carbon-limited chemostat cultures.	FEMS Yeast Res	2005	15949974
Diauxic shift time course (Batch1)	13	"Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) time course samples were grown in batch for the indicated time. The Low-D chemostat vs. High-D chemostat hybridization's channel 2 sample was grown in a chemostat, with a dilution rate of 0.05 volumes/hour; it is most similar to the time course samples taken between 8 and 9 hours."	Brauer MJ	"Brauer MJ, Saldanha AJ, Dolinski K, Botstein D"	Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.	Mol Biol Cell	2005	15758028
Diauxic shift time course (Batch2)	7	"Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) samples were grown in batch for the indicated time."	Brauer MJ	"Brauer MJ, Saldanha AJ, Dolinski K, Botstein D"	Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.	Mol Biol Cell	2005	15758028
Transcriptional regulation (I)	40	several crosses of BY4716 and wild wine strain	Brem RB	"Brem RB, Yvert G, Clinton R, Kruglyak L"	Genetic dissection of transcriptional regulation in budding yeast.	Science	2002	11923494
Transcriptional regulation (I)(dye swap)	40	several crosses of BY4716 and wild wine strain	Brem RB	"Brem RB, Yvert G, Clinton R, Kruglyak L"	Genetic dissection of transcriptional regulation in budding yeast.	Science	2002	11923494
Transcriptional regulation (II)	12	independent cultures of BY4716 and wild strains against a reference pool of BY4716	Brem RB	"Brem RB, Yvert G, Clinton R, Kruglyak L"	Genetic dissection of transcriptional regulation in budding yeast.	Science	2002	11923494
Transcriptional regulation (II)(dye swap)	11	independent cultures of BY4716 and wild strains against a reference pool of BY4716	Brem RB	"Brem RB, Yvert G, Clinton R, Kruglyak L"	Genetic dissection of transcriptional regulation in budding yeast.	Science	2002	11923494
Genetic variation in gene expression among parents and progenies (dye-swap)	131	"Expression profiling of parental strains and 112 haploid progenies from a cross of strain BY4716 and the wild wine strain RM11-1a. Results used to find linkage between gene expression levels, which are treated as quantitative traits, and genetic markers."	Brem RB	"Brem RB, Kruglyak L"	"The landscape of genetic complexity across 5,700 gene expression traits in yeast."	Proc Natl Acad Sci U S A	2005	15659551
Genetic variation in gene expression among parents and progenies	131	"Expression profiling of parental strains and 112 haploid progenies from a cross of strain BY4716 and the wild wine strain RM11-1a. Results used to find linkage between gene expression levels, which are treated as quantitative traits, and genetic markers."	Brem RB	"Brem RB, Kruglyak L"	"The landscape of genetic complexity across 5,700 gene expression traits in yeast."	Proc Natl Acad Sci U S A	2005	15659551
Lithium response	7	"Wild type CEN.PK113-7D grown with 20 g/L galactose. LiCl (10 mM, therapeutically relevant) added and samples analyzed at 0, 20, 40, 60 and 140 minutes after LiCl addition. Lithium inhibits phosphoglucomutase, affecting galactose uptake and growth."	Bro C	"Bro C, Regenberg B, Lagniel G, Labarre J, Montero-Lomeli M, Nielsen J"	"Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells."	J Biol Chem	2003	12791685
Chitin synthesis	11	wt and fks1 mutant exposed to chitin-inducing glucosamine for 2-hours or continuous steady state	Bulik DA	"Bulik DA, Olczak M, Lucero HA, Osmond BC, Robbins PW, Specht CA"	Chitin synthesis in Saccharomyces cerevisiae in response to supplementation of growth medium with glucosamine and cell wall stress.	Eukaryot Cell	2003	14555471
Genotoxic stress	24	"BY4730 cells treated with DNA-reactive compounds cisplatin, methyl methanesulfonate (MMS), and bleomycin to induce genotoxic stress. Effect of genotoxic compounds compared to cytotoxic compounds, NaCl and ethanol."	Caba E	"Caba E, Dickinson DA, Warnes GR, Aubrecht J"	Differentiating mechanisms of toxicity using global gene expression analysis in Saccharomyces cerevisiae.	Mutat Res	2005	15878181
H2O2 exposure to wt and Deltatrr1 knockout	15	Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae.	Carmel-Harel O	"Carmel-Harel O, Stearman R, Gasch AP, Botstein D, Brown PO, Storz G"	Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae.	Mol Microbiol	2001	11169101
pho85 inhibition	12	we used a chemical genetic approach that enabled us to control Pho85 kinase activity with a cell-permeable inhibitor and whole genome transcript profiling.	Carroll AS	"Carroll AS, Bishop AC, DeRisi JL, Shokat KM, O'Shea EK"	Chemical inhibition of the Pho85 cyclin-dependent kinase reveals a role in the environmental stress response.	Proc Natl Acad Sci U S A	2001	11675494
Unfolded protein response	2	DNA microarray assays to examine whether the expression of H-2Kb increases the transcription of genes also induced by the UPR. mRNA was harvested from wild-type cells that either express H-2Kb or bear a control plasmid	Casagrande R	"Casagrande R, Stern P, Diehn M, Shamu C, Osario M, Zuniga M, Brown PO, Ploegh H"	Degradation of proteins from the ER of S. cerevisiae requires an intact unfolded protein response pathway.	Mol Cell	2000	10882108
acid response	11	"response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity"	Causton HC	"Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA"	Remodeling of yeast genome expression in response to environmental changes.	Mol Biol Cell	2001	11179418
alkali response	8	"response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity"	Causton HC	"Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA"	Remodeling of yeast genome expression in response to environmental changes.	Mol Biol Cell	2001	11179418
heat response	7	"response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity"	Causton HC	"Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA"	Remodeling of yeast genome expression in response to environmental changes.	Mol Biol Cell	2001	11179418
NaCl response	6	"response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity"	Causton HC	"Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA"	Remodeling of yeast genome expression in response to environmental changes.	Mol Biol Cell	2001	11179418
peroxide response	7	"response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity"	Causton HC	"Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA"	Remodeling of yeast genome expression in response to environmental changes.	Mol Biol Cell	2001	11179418
Sorbitol response	6	"response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity"	Causton HC	"Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA"	Remodeling of yeast genome expression in response to environmental changes.	Mol Biol Cell	2001	11179418
TBP inhibition	20	"Here, we use DNA microarrays to explore the genome-wide interplay of several TBP-interacting inhibitors in the yeast Saccharomyces cerevisiae"	Chitikila C	"Chitikila C, Huisinga KL, Irvin JD, Basehoar AD, Pugh BF"	Interplay of TBP inhibitors in global transcriptional control.	Mol Cell	2002	12419230
mitotic cell cycle	17	Cell-cycle arrested yeast cells are synchronized by being held at a restrictive temperature and then released at t=0. RNA expression via Affymetrix chips is measured every 10 minutes until t=160. Data up to t=40 reflects temperature-induced as well as cell-cycle effects.	Cho RJ	"Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW"	A genome-wide transcriptional analysis of the mitotic cell cycle.	Mol Cell	1998	9702192
Sporulation time course	7	Samples taken during sporulation up to 11 hours	Chu S	"Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I"	The transcriptional program of sporulation in budding yeast.	Science	1998	9784122
mRNA processing factors and splicing (dye swap)	17	"brr1, cus2, dbr1, ecm2, gcr3, hsp104, msl1, mud1, mud13, mud2, nam8, prp17, prp18, snu17, snu40, snu66, upf3 deletion mutants"	Clark TA	"Clark TA, Sugnet CW, Ares M"	Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays.	Science	2002	11988574
mRNA processing factors and splicing	17	"brr1, cus2, dbr1, ecm2, gcr3, hsp104, msl1, mud1, mud13, mud2, nam8, prp17, prp18, snu17, snu40, snu66, upf3 deletion mutants"	Clark TA	"Clark TA, Sugnet CW, Ares M"	Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays.	Science	2002	11988574
yap1 and yap2 knockouts with peroxide and cadmium added	11	"There is a separate summary series for each strain and treatment combination. These include wild type control, with peroxide and with cadmium, yap1 knockout control and with peroxide and with cadmium, yap2 knockout control and with peroxide and with cadmium, double knockouts control and with peroxide, wild type and fold change numbers from wild type control for each strain and treatment."	Cohen BA	"Cohen BA, Pilpel Y, Mitra RD, Church GM"	Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks.	Mol Biol Cell	2002	12006656
Osmotic stress	12	Comparison of wild type and rpd3- S. cerevisiae cells in response to osmotic stress. Wild type (MATalpha ura3 leu2 his3) and rpd3- (MATalpha ura3 leu2 his3 rpd3::KANMX) were grown to OD660=1 in YPD media and then subjected or not to a brief osmotic stress (5 or 20 min / 0.4 M NaCl). Cells were collected by centrifugation and total RNA was extracted as described.	De Nadal E	"De Nadal E, Zapater M, Alepuz PM, Sumoy L, Mas G, Posas F"	The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes.	Nature	2004	14737171
Diauxic shift time course	7	Samples of expression taken at several time points during the metabolic shift from anaerobic fermentation to aerobic respiration.	DeRisi JL	"DeRisi JL, Iyer VR, Brown PO"	Exploring the metabolic and genetic control of gene expression on a genomic scale.	Science	1997	9381177
"post heat shock, delayed rapamycin exposure time course"	20	we have examined the role of the essential protein Tap42 in transcriptional regulation by Tor	Duvel K	"Duvel K, Santhanam A, Garrett S, Schneper L, Broach JR"	Multiple roles of Tap42 in mediating rapamycin-induced transcriptional changes in yeast.	Mol Cell	2003	12820961
"post heat shock, immediate rapamycin exposure time course"	10	we have examined the role of the essential protein Tap42 in transcriptional regulation by Tor	Duvel K	"Duvel K, Santhanam A, Garrett S, Schneper L, Broach JR"	Multiple roles of Tap42 in mediating rapamycin-induced transcriptional changes in yeast.	Mol Cell	2003	12820961
Mitochondrial dysfunction	11	We used DNA microarrays to characterize the transcriptional responses to different mitochondrial perturbations in Saccharomyces cerevisiae.	Epstein CB	"Epstein CB, Waddle JA, Hale W, Dave V, Thornton J, Macatee TL, Garner HR, Butow RA"	Genome-wide responses to mitochondrial dysfunction.	Mol Biol Cell	2001	11179416
SPT10 global transcription regulator null mutant	6	Expression profiling of mutants lacking Spt10p. Spt10p binds the upstream activating sequences in all major core histone promoters. Results provide insight into the mechanism by which Spt10p acts as a global regulator of transcription.	Eriksson PR	"Eriksson PR, Mendiratta G, McLaughlin NB, Wolfsberg TG, Marino-Ramirez L, Pompa TA, Jainerin M, Landsman D, Shen CH, Clark DJ"	Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements.	Mol Cell Biol	2005	16199888
Evolved strains	4	"Beginning with a clonal, founding population, independently evolved strains were obtained from three independent cultures after continuous aerobic growth in glucose-limited chemostats for more than 250 generations. DNA microarrays were used to compare genome-wide patterns of gene expression in the evolved strains and the parental strain."	Ferea TL	"Ferea TL, Botstein D, Brown PO, Rosenzweig RF"	Systematic changes in gene expression patterns following adaptive evolution in yeast.	Proc Natl Acad Sci U S A	1999	10449761
Hydrostatic pressure response	2	Gene expression patterns in response to hydrostatic pressure were determined by whole genome microarray hybridization. Functional classification of the 274 genes affected by pressure treatment of 200 MPa for 30 min revealed a stress response expression profile.	Fernandes PM	"Fernandes PM, Domitrovic T, Kao CM, Kurtenbach E"	Genomic expression pattern in Saccharomyces cerevisiae cells in response to high hydrostatic pressure.	FEBS Lett	2004	14706843
proteasome inhibition with exposure to PS-341	30	whole-genome technologies in Saccharomyces cerevisiae to determine the cellular impact of the proteasome inhibitor PS-341	Fleming JA	"Fleming JA, Lightcap ES, Sadis S, Thoroddsen V, Bulawa CE, Blackman RK"	Complementary whole-genome technologies reveal the cellular response to proteasome inhibition by PS-341.	Proc Natl Acad Sci U S A	2002	11830665
Aging in yeast	8	"wt & sgs1 null, w/ or w/o MMS (DNA damaging agent)"	Fry RC	"Fry RC, Sambandan TG, Rha C"	DNA damage and stress transcripts in Saccharomyces cerevisiae mutant sgs1.	Mech Ageing Dev	2003	12875747
"Amino acid, adenine starvation "	5	"minimal medium lacking amino acids and adenine, samples at 0, 0.5, 1, 2, 4, 6 hours"	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Carbon sources	6	"wt grown in YP media with 2% weight to volume of glucose, raffinose, galactose, fructose, sucrose, or ethanol as carbon source"	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Diamide treatment time course	8	"Diamide (1.5 mM) added to culture, and samples recovered at several time points up to 90 minutes."	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Dithiothrietol exposure time course (y13)	8	Dithiothrietol (DTT; 2.5 mM) added to culture and samples recovered at several time points up to 180 minutes.	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Dithiothrietol exposure time course (y14)	7	Dithiothrietol (DTT; 2.5 mM) added to culture and samples recovered at several time points up to 480 minutes.	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Hydrogen peroxide response	2	wt and yap1 mutant collected 20 minutes after exposure to 0.3mM hydrogren peroxide	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Hydrogen peroxide response time course	9	Hydrogen peroxide (0.3 mM) added to culture and samples taken at several time points up to 160 minutes.	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Heat Shock 25C to 37C time course	8	Heat shock from 25¡C to 37¡C. Samples collected at several time points up to 80 minutes.	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Heat Shock 29C to 33C time course	4	"Heat shock from 29¡C to 33¡C. Samples collected at 5, 15, 30 and 90 minutes."	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Heat Shock 30C to 37C time course	5	"Cultures shifted from 30¡C to 37¡C and samples collected at 0, 5, 15, 30 and 60 minutes."	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Heat Shock 37C to 25C	5	"Heat shock from 37¡C to 25¡C. Samples collected at 15, 30, 45, 60 and 90 minutes."	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Mild Heat Shock	6	"Heat shock from 29¡C to 33¡C, with or without addition of 1 M sorbitol. Samples collected at 5, 15 and 30 minutes."	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Heat Shock from various temp to 37C	6	"Samples collected 20 min after temperature shift from either 17¡C, 21¡C, 25¡C, 29¡C or 33¡C to 37¡C."	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Hyper-osmotic shock time course	6	Samples grown in YPD supplemented with 1 M sorbitol and collected at several time points up to 60 minutes.	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Hypo-osmotic shock time course	5	"Cells resuspended in YPD medium without sorbitol. Samples recovered at 5, 15, 30, 45 and 60 minutes."	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Menadione exposure time course	9	Superoxide-generating drug menadione bisulphate (1 mM) added to culture and samples removed at several time points up to 160 minutes.	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Nitrogen depletion time course	9	"Samples grown in minimal medium without amino acids or adenine, low ammonium sulfate and collected at various time points up to 3 days."	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Stationary phase time course (y12)	10	Culture grown to OD600 0.3 after which samples collected at various time points up to 13 days	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Stationary phase time course (y14)	9	Culture grown to OD600 0.3 after which samples collected at various time points up to 13 days	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Steady-state temperature (y13)	5	"Samples collected from cells grown continuously at 17¡C, 21¡C, 25¡C, 29¡C and 37¡C, and compared to cells grown at 33¡C"	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Steady-state temperature (y14)	8	"Samples collected from cells grown continuously at 15¡C, 17¡C, 21¡C, 25¡C, 29¡C, 33¡C and 36¡C"	Gasch AP	"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO"	Genomic expression programs in the response of yeast cells to environmental changes.	Mol Biol Cell	2000	11102521
Copper regulon	6	"Growth conditions of excess copper or copper deficiency, regulated by Mac1 or Ace1 transcriptional activators."	Gross C	"Gross C, Kelleher M, Iyer VR, Brown PO, Winge DR"	Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays.	J Biol Chem	2000	10922376
rapamycin exposure	14	We measured the immediate transcriptional response of yeast grown in rich media and treated with rapamycin to investigate the direct effects of Tor proteins on nutrient-sensitive signaling pathways	Hardwick JS	"Hardwick JS, Kuruvilla FG, Tong JK, Shamji AF, Schreiber SL"	Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins.	Proc Natl Acad Sci U S A	1999	10611304
pho85 related knockouts	20	DNA microarrays to examine the genome-wide transcriptional consequences of deleting PHO85 or members of the Pho85 cyclin family	Huang D	"Huang D, Moffat J, Andrews B"	Dissection of a complex phenotype by functional genomics reveals roles for the yeast cyclin-dependent protein kinase Pho85 in stress adaptation and cell integrity.	Mol Cell Biol	2002	12077337
diverse knockout mutants	300	300 knockout mutants create a compendium of expression profiles	Hughes TR	"Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH"	Functional discovery via a compendium of expression profiles.	Cell	2000	10929718
GAL mutants	21	systematic perturbations of the yeast galactose-utilization pathway	Ideker T	"Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L"	Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.	Science	2001	11340206
SBF-MBF genomic distribution (ORF_intergenic_v1.0) (I)	2	Identification of genomic binding sites of the sequence-specific transcription factors SBF and MBF.	Iyer VR	"Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO"	Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.	Nature	2001	11206552
SBF-MBF genomic distribution (ORF_intergenic_v1.0) (II)	2	Identification of genomic binding sites of the sequence-specific transcription factors SBF and MBF.	Iyer VR	"Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO"	Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.	Nature	2001	11206552
SBF-MBF genomic distribution (intergenic_v1.0) (I)	6	Identification of genomic binding sites of the sequence-specific transcription factors SBF and MBF.	Iyer VR	"Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO"	Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.	Nature	2001	11206552
SBF-MBF genomic distribution (intergenic_v1.0) (II)	5	Identification of genomic binding sites of the sequence-specific transcription factors SBF and MBF.	Iyer VR	"Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO"	Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.	Nature	2001	11206552
"Exposure to alkylating, oxidizing agents, ionizing radiation"	28	"Exposure to carcinogenic alkylating agents, oxidizing agents, and ionizing radiation modulates transcript levels for over one third of Saccharomyces cerevisiae's 6,200 genes."	Jelinsky SA	"Jelinsky SA, Estep P, Church GM, Samson LD"	Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes.	Mol Cell Biol	2000	11027285
Xylose metabolism	6	"Strain YSX3 engineered for D-xylose utilization and respiration-deficient mutant FPL-YSX3P were grown under full aeration or oxygen limitation, with glucose or xylose as a carbon source."	Jin YS	"Jin YS, Laplaza JM, Jeffries TW"	Saccharomyces cerevisiae engineered for xylose metabolism exhibits a respiratory response.	Appl Environ Microbiol	2004	15528549
Ras/cAMP signal transduction pathway (dye swap)	5	"wt, pde2Delta deletion mutant"	Jones DL	"Jones DL, Petty J, Hoyle DC, Hayes A, Ragni E, Popolo L, Oliver SG, Stateva LI"	Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway.	Physiol Genomics	2003	14570984
Ras/cAMP signal transduction pathway	5	"wt, pde2Delta deletion mutant"	Jones DL	"Jones DL, Petty J, Hoyle DC, Hayes A, Ragni E, Popolo L, Oliver SG, Stateva LI"	Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway.	Physiol Genomics	2003	14570984
Haa1 analysis	4	Microarray experiments were carried out to determine whether Haa1 is a transcription factor and to identify any potential target genes. Haa1 was found to be a transcriptional activator of a set of genes encoding membrane stress proteins.	Keller G	"Keller G, Ray E, Brown PO, Winge DR"	"Haa1, a protein homologous to the copper-regulated transcription factor Ace1, is a novel transcriptional activator."	J Biol Chem	2001	11504737
Carbon source shift	3	The global gene expression program that accompanies the adaptation of Saccharomyces cerevisiae to an abrupt transfer from a fermentable to a nonfermentable carbon source was characterized by using a cDNA microarray to monitor the relative abundances and polysomal distributions of mRNAs.	Kuhn KM	"Kuhn KM, DeRisi JL, Brown PO, Sarnow P"	Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source.	Mol Cell Biol	2001	11154278
Unfolded protein response and HAC1 transcription	13	"Strains expressing HAC1 grown at 30C or shifted from 23C to 37C, and treated with 6mM DTT or tunicamycin for 60 minutes.  DTT and TM activate the unfolded protein response, which is regulated by Hac1p."	Leber JH	"Leber JH, Bernales S, Walter P"	IRE1-independent gain control of the unfolded protein response.	PLoS Biol	2004	15314654
rnt1 null mutant expression profile	9	"Expression profiling of isogenic strains lacking Rnt1p, a member of the RNase III family of double-stranded RNA endonucleases. Results identify potential Rnt1p mRNA targets"	Lee A	"Lee A, Henras AK, Chanfreau G"	Multiple RNA surveillance pathways limit aberrant expression of iron uptake mRNAs and prevent iron toxicity in S. cerevisiae.	Mol Cell	2005	15989963
"gcr1 mutant, glucose exposure"	17	"the genomic expression patterns of wild-type and gcr1 mutant yeast growing on various media, with and without glucose"	Lopez MC	"Lopez MC, Baker HV"	Understanding the growth phenotype of the yeast gcr1 mutant in terms of global genomic expression patterns.	J Bacteriol	2000	10940042
"Zinc homeostatis, zap1"	9	"The Zap1p transcription factor senses cellular zinc status and increases expression of its target genes in response to zinc deficiency. Previously known Zap1p-regulated genes encode the Zrt1p, Zrt2p, and Zrt3p zinc transporter genes and Zap1p itself. To allow the characterization of additional genes in yeast important for zinc homeostasis, a systematic study of gene expression on the genome-wide scale was used to identify other Zap1p target genes. Using a combination of DNA microarrays and a computer-assisted analysis of shared motifs in the promoters of similarly regulated genes, we identified 46 genes that are potentially regulated by Zap1p. Zap1p-regulated expression of seven of these newly identified target genes was confirmed independently by using lacZ reporter fusions, suggesting that many of the remaining candidate genes are also Zap1p targets. Our studies demonstrate the efficacy of this combined approach to define the regulon of a specific eukaryotic transcription factor."	Lyons TJ	"Lyons TJ, Gasch AP, Gaither LA, Botstein D, Brown PO, Eide DJ"	Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast.	Proc Natl Acad Sci U S A	2000	10884426
MAPK mutants	11	transcript levels in strains in which MAPK signaling was altered genetically	Madhani HD	"Madhani HD, Galitski T, Lander ES, Fink GR"	Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants.	Proc Natl Acad Sci U S A	1999	10535956
TOR2-controlled transcription	12	Comparison of total transcription profiles for temperature-sensitive TOR2 mutant strain SH121 to its isogenic wild type counterpart SH100	Martin DE	"Martin DE, Demougin P, Hall MN, Bellis M"	"Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data."	BMC Bioinformatics	2004	15476558
immunosuppressant response	7	"treatment of yeast mutant strains defective in calcineurin, immunophilins or other genes with the immunosuppressants cyclosporin A or FK506"	Marton MJ	"Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE, Hartwell LH, Brown PO, Friend SH"	Drug target validation and identification of secondary drug target effects using DNA microarrays.	Nat Med	1998	9809554
abf1-1 mutant at 36C	4	"abf1-1 mutant and wt cells grown at 30C, raised to 36C for 45 min.  Four repeats of the same experiement."	Miyake T	"Miyake T, Reese J, Loch CM, Auble DT, Li R"	Genome-wide analysis of ARS (autonomously replicating sequence) binding factor 1 (Abf1p)-mediated transcriptional regulation in Saccharomyces cerevisiae.	J Biol Chem	2004	15192094
Phosphate-regulated pathway (I)	5	"Modifying phosphate levels through mutation (pho81c, pho85, pho80, pho4c) or chemical manipulation"	Ogawa N	"Ogawa N, DeRisi J, Brown PO"	New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis.	Mol Biol Cell	2000	11102525
Phosphate-regulated pathway (II)	3	Modifying phosphate levels through mutation or chemical manipulation (YPAD+Pi vs. YPAD-Pi)	Ogawa N	"Ogawa N, DeRisi J, Brown PO"	New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis.	Mol Biol Cell	2000	11102525
Fermentation time course	12	Expression of brewing yeast during production scale lager beer fermentation.  Samples at time points up to 264 hours.	Olesen K	"Olesen K, Felding T, Gjermansen C, Hansen J"	The dynamics of the Saccharomyces carlsbergensis brewing yeast transcriptome during a production-scale lager beer fermentation.	FEMS Yeast Res	2002	12702272
Deubiquitinating enzyme UBP10 inactivation	4	"Comparison of wt, ubp10 null, sir4 null, and ubp10 sir4 double null mutants"	Orlandi I	"Orlandi I, Bettiga M, Alberghina L, Vai M"	Transcriptional profiling of ubp10 null mutant reveals altered subtelomeric gene expression and insurgence of oxidative stress response.	J Biol Chem	2004	14623890
HOG MAPK pathway	133	response to elevated osmolarity	O'Rourke SM	"O'Rourke SM, Herskowitz I"	Unique and redundant roles for HOG MAPK pathway components as revealed by whole-genome expression analysis.	Mol Biol Cell	2004	14595107
Phosphomannose isomerase PMI40 deletion strain response to excess mannose	15	Expression profiling of a phosphomannose isomerase PMI40 deletion strain growing on media with various mannose concentrations up to 5 g/liter. Results provide insight into the cause of slow growth exhibited by the PMI40 deletion strain in media with excess mannose.	Pitkanen JP	"Pitkanen JP, Torma A, Alff S, Huopaniemi L, Mattila P, Renkonen R"	Excess mannose limits the growth of phosphomannose isomerase PMI40 deletion strain of Saccharomyces cerevisiae.	J Biol Chem	2004	15520001
Sporulation of two strains	24	"meiotic expression patterns of two yeast strains, SK1 and W303, that display distinct kinetics and efficiencies of sporulation"	Primig M	"Primig M, Williams RM, Winzeler EA, Tevzadze GG, Conway AR, Hwang SY, Davis RW, Esposito RE"	The core meiotic transcriptome in budding yeasts.	Nat Genet	2000	11101837
Filamentous-form growth on solid media time course	10	wt diploid cells shifted from yeast-form growth in SHAD liquid with plentiful glucose and ammonium to filamentous-form growth on SLAD agar with low ammonium.  Samples collected hourly for 10 hours.	Prinz S	"Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, Galitski T"	Control of yeast filamentous-form growth by modules in an integrated molecular network.	Genome Res	2004	14993204
Iron concentration and AFT1 overexpression	4	"Analysis of iron-regulated gene expression in Saccharomyces cerevisiae using cDNA microarrays has identified three putative cell wall proteins that are directly regulated by Aft1p, the major iron-dependent transcription factor in yeast."	Protchenko O	"Protchenko O, Ferea T, Rashford J, Tiedeman J, Brown PO, Botstein D, Philpott CC"	Three cell wall mannoproteins facilitate the uptake of iron in Saccharomyces cerevisiae.	J Biol Chem	2001	11673473
Pheremone response	56	"Exposure of MATa to alpha-factor, MATalpha to a-factor time courses at various concentrations of pheremones"	Roberts CJ	"Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, Tyers M, Boone C, Friend SH"	Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles.	Science	2000	10657304
"TPK1, TPK2, TPK3 mutants"	12	"study of TPK1 (alternate name for YJL164C), TPK2 (alternate name for YPL203W), and TPK3 (YRL166C) mutants"	Robertson LS	"Robertson LS, Causton HC, Young RA, Fink GR"	The yeast A kinases differentially regulate iron uptake and respiratory function.	Proc Natl Acad Sci U S A	2000	10811893
sus1 mutant	6	"wt, sus1 deletion mutant"	Rodriguez-Navarro S	"Rodriguez-Navarro S, Fischer T, Luo MJ, Antunez O, Brettschneider S, Lechner J, Perez-Ortin JE, Reed R, Hurt E"	"Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery."	Cell	2004	14718168
fhl1 and ifh1 deletion mutants	6	Expression profiling of fhl1 single deletion mutant and ifh1 fhl1 double deletion mutant. Mutants generated from W303 strain. Results indicate that Ifh1p and Fhl1p function together to regulate the transcription of ribosomal protein genes.	Rudra D	"Rudra D, Zhao Y, Warner JR"	Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins.	EMBO J	2005	15692568
Iron homeostasis	2	DNA microarrays were used to identify genes regulated by AFT2	Rutherford JC	"Rutherford JC, Jaron S, Ray E, Brown PO, Winge DR"	A second iron-regulatory system in yeast independent of Aft1p.	Proc Natl Acad Sci U S A	2001	11734641
Histone deacetylase RPD3 deletion and histone mutations	18	"Analysis of gene regulation by expression profiling of single mutants for histone deacetylase RPD3, histones H3 and H4, and double mutants for either RPD3 and H3 or RPD3 and H4. Histone mutants defective in amino terminal tails, which are acetylated and deacetylated in transcription regulation."	Sabet N	"Sabet N, Volo S, Yu C, Madigan JP, Morse RH"	Genome-wide analysis of the relationship between transcriptional regulation by Rpd3p and the histone H3 and H4 amino termini in budding yeast.	Mol Cell Biol	2004	15456858
limitation by Leucine	29	physiological response to limitation by leucine in batch and steady-state (chemostat) cultures of S. cerevisiae	Saldanha AJ	"Saldanha AJ, Brauer MJ, Botstein D"	Nutritional homeostasis in batch and steady-state culture of yeast.	Mol Biol Cell	2004	15240820
limitation by Phosphate	30	physiological response to limitation by phosphate in batch and steady-state (chemostat) cultures of S. cerevisiae	Saldanha AJ	"Saldanha AJ, Brauer MJ, Botstein D"	Nutritional homeostasis in batch and steady-state culture of yeast.	Mol Biol Cell	2004	15240820
limitation by Sulfate	21	physiological response to limitation by sulfate in batch and steady-state (chemostat) cultures of S. cerevisiae	Saldanha AJ	"Saldanha AJ, Brauer MJ, Botstein D"	Nutritional homeostasis in batch and steady-state culture of yeast.	Mol Biol Cell	2004	15240820
limitation by Uracil	20	physiological response to limitation by Uracil in batch and steady-state (chemostat) cultures of S. cerevisiae	Saldanha AJ	"Saldanha AJ, Brauer MJ, Botstein D"	Nutritional homeostasis in batch and steady-state culture of yeast.	Mol Biol Cell	2004	15240820
"comparison of limitation by Ura, Sul, Pho, and Leu"	24	physiological response to limitation by diverse nutrients in steady-state (chemostat) cultures of S. cerevisiae	Saldanha AJ	"Saldanha AJ, Brauer MJ, Botstein D"	Nutritional homeostasis in batch and steady-state culture of yeast.	Mol Biol Cell	2004	15240820
Pre-mRNA splicing factor mutants at restrictive temperature time course	24	"wt, prp17 null, prp17-1, prp22-1 at time points following a temperature shift from permissive 23C to restrictive 37C"	Sapra AK	"Sapra AK, Arava Y, Khandelia P, Vijayraghavan U"	"Genome-wide analysis of pre-mRNA splicing: intron features govern the requirement for the second-step factor, Prp17 in Saccharomyces cerevisiae and Schizosaccharomyces pombe."	J Biol Chem	2004	15452114
IFH1 overexpression: time course	24	Analysis of overexpression of essential ribosomal protein activator IFH1. Cells engineered to express IFH1 from a galactose inducible promoter. Expression examined at various time points up to 60 minutes following galactose addition. Results indicate that IFH1 regulates ribosomal protein genes.	Schawalder SB	"Schawalder SB, Kabani M, Howald I, Choudhury U, Werner M, Shore D"	Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1.	Nature	2004	15616569
"Heat Shock, kin82 mutant"	10	"wt and kin82 mutant strains after heat shock from 25C to 37C, samples at time points up to 1 hour."	Segal E	"Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N"	Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.	Nat Genet	2003	12740579
"Hypo-osmotic shock, ppt1 mutant"	10	"Temporal analysis of wild type and ppt1 mutant strains after hypo-osmotic shock. Cultures grown with 1M sorbitol for ~20 hours, then cells resuspended in YPD after which samples collected at several time points up to 1 hour."	Segal E	"Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N"	Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.	Nat Genet	2003	12740579
"Stationary phase, ypl230w mutant"	12	"wt, ypl230w mutant in stationary phase. Cultures were grown to OD600 of 0.27 (ypl230w) and 0.4 (wild-type), then samples collected at various time points up to 24 hours"	Segal E	"Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N"	Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.	Nat Genet	2003	12740579
Iron deprivation	6	Saccharomyces cerevisiae responds to depletion of iron in the environment	Shakoury-Elizeh M	"Shakoury-Elizeh M, Tiedeman J, Rashford J, Ferea T, Demeter J, Garcia E, Rolfes R, Brown PO, Botstein D, Philpott CC"	Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.	Mol Biol Cell	2004	14668481
oxidative stress responses	70	"Oxidative stress caused by Menadione or Hydrogen peroxide in synchronized Saccharomyces cerevisiae cultures. Alpha factor synchronized cultures (0.2-0.4 OD), treated at the beginning of S phase (25 min after release from G1 arrest) with either 2 mM Menadione (MD) or 0.24 mM Hydrogen peroxide (HP), show cell cycle effects. Cells treated with MD arrested at G1. Cells treated with HP delayed at S and then, after removal of HP at 135 minutes , continued the cell cycle, only to arrest at G2/M. Growth was carried out in 30C with shaking (295 rpm)."	Shapira M	"Shapira M, Segal E, Botstein D"	Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress.	Mol Biol Cell	2004	15371544
"Cell cycle, alpha-factor block-release"	16	"Culture synchronized by alpha factor arrest, then samples taken every 7 minutes as cells went through cell cycle."	Spellman PT	"Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B"	Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.	Mol Biol Cell	1998	9843569
"Cell cycle, cdc15 block-release"	25	Culture synchronized in telophase by arrest of cdc15 temperature-sensitive mutant. Samples taken during the course of almost three full cell cycles.	Spellman PT	"Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B"	Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.	Mol Biol Cell	1998	9843569
Cyclin overexpression	2	Cells arrested in G1 for CLN3 overexpression.	Spellman PT	"Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B"	Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.	Mol Biol Cell	1998	9843569
"Cell cycle, elutriation"	14	Culture synchronized by elutriation and samples removed at several time points up to 6.5 h.	Spellman PT	"Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B"	Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.	Mol Biol Cell	1998	9843569
Snf/Swi mutants (v1_2.2)	2	"swi1, swi2 deletion mutants"	Sudarsanam P	"Sudarsanam P, Iyer VR, Brown PO, Winston F"	Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae.	Proc Natl Acad Sci U S A	2000	10725359
Snf/Swi mutants (384_F_v1.0)	8	"snf2, swi1 deletion mutants grown in minimal or rich media"	Sudarsanam P	"Sudarsanam P, Iyer VR, Brown PO, Winston F"	Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae.	Proc Natl Acad Sci U S A	2000	10725359
Nutrient limitation under aerobic and anaerobic conditions	24	"Expression profiling of MATa CEN.PK113-7D chemostat cultures grown either aerobically or anaerobically in media limited for either glucose, nitrogen, phosphorous, or sulfur. Results provide insight into the interaction between oxygen and nutrient responsive pathways."	Tai SL	"Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran JM, Pronk JT"	Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae.	J Biol Chem	2005	15496405
Ssl1 mutant for a subunit of TFIIH response to methyl methanesulfonate	12	Analysis of Ssl1 mutant for a subunit of TFIIH treated with methyl methanesulfonate (MMS). Ssl1 mutant contains C406A substitution and is sensitive to DNA damaging agents such as MMS	Takagi Y	"Takagi Y, Masuda CA, Chang WH, Komori H, Wang D, Hunter T, Joazeiro CA, Kornberg RD"	Ubiquitin ligase activity of TFIIH and the transcriptional response to DNA damage.	Mol Cell	2005	15837426
Ume6 regulon (Ye6100subA)	8	"wt, ume6 deletion diploids during vegetative growth in glucose and acetate"	Williams RM	"Williams RM, Primig M, Washburn BK, Winzeler EA, Bellis M, Sarrauste de Menthiere C, Davis RW, Esposito RE"	The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast.	Proc Natl Acad Sci U S A	2002	12370439
Ume6 regulon (Ye6100subB)	8	"wt, ume6 deletion diploids during vegetative growth in glucose and acetate"	Williams RM	"Williams RM, Primig M, Washburn BK, Winzeler EA, Bellis M, Sarrauste de Menthiere C, Davis RW, Esposito RE"	The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast.	Proc Natl Acad Sci U S A	2002	12370439
Ume6 regulon (Ye6100subC)	8	"wt, ume6 deletion diploids during vegetative growth in glucose and acetate"	Williams RM	"Williams RM, Primig M, Washburn BK, Winzeler EA, Bellis M, Sarrauste de Menthiere C, Davis RW, Esposito RE"	The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast.	Proc Natl Acad Sci U S A	2002	12370439
Ume6 regulon (Ye6100subD)	8	"wt, ume6 deletion diploids during vegetative growth in glucose and acetate"	Williams RM	"Williams RM, Primig M, Washburn BK, Winzeler EA, Bellis M, Sarrauste de Menthiere C, Davis RW, Esposito RE"	The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast.	Proc Natl Acad Sci U S A	2002	12370439
Heat shock transcription factor 1 mutant response to heat stress	4	Analysis of a heat shock transcription factor 1 (HSF1) temperature sensitive mutant strain subjected to heat stress at 33 degrees C. HSF1 mutant contains an arginine to serine and a phenylalanine to serine substitution at residues 206 and 256 respectively. Results identify novel targets of HSF1.	Yamamoto A	"Yamamoto A, Mizukami Y, Sakurai H"	Identification of a novel class of target genes and a novel type of binding sequence of heat shock transcription factor in Saccharomyces cerevisiae.	J Biol Chem	2005	15647283
Transcription factor deletions	7	Study expression effects of single transcription factor deletions.	Yeang CH	"Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T"	Validation and refinement of gene-regulatory pathways on a network of physical interactions.	Genome Biol	2005	15998451
Ca(2+) exposure	24	"n Saccharomyces cerevisiae, the Ca(2+)/calmodulin-dependent protein phosphatase, calcineurin, is activated by specific environmental conditions, including exposure to Ca(2+) and Na(+), and induces gene expression by regulating the Crz1p/Tcn1p transcription factor. We used DNA microarrays to perform a comprehensive analysis of calcineurin/Crz1p-dependent gene expression following addition of Ca(2+) (200 mm) or Na(+) (0.8 m) to yeast."	Yoshimoto H	"Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS"	Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.	J Biol Chem	2002	12058033
Na(+) exposure	16	"n Saccharomyces cerevisiae, the Ca(2+)/calmodulin-dependent protein phosphatase, calcineurin, is activated by specific environmental conditions, including exposure to Ca(2+) and Na(+), and induces gene expression by regulating the Crz1p/Tcn1p transcription factor. We used DNA microarrays to perform a comprehensive analysis of calcineurin/Crz1p-dependent gene expression following addition of Ca(2+) (200 mm) or Na(+) (0.8 m) to yeast."	Yoshimoto H	"Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS"	Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.	J Biol Chem	2002	12058033
Iron uptake	4	"In the yeast Saccharomyces cerevisiae, uptake of iron is largely regulated by the transcription factor Aft1. cDNA microarrays were used to identify new iron and AFT1-regulated genes."	Yun CW	"Yun CW, Ferea T, Rashford J, Ardon O, Brown PO, Botstein D, Kaplan J, Philpott CC"	Desferrioxamine-mediated iron uptake in Saccharomyces cerevisiae. Evidence for two pathways of iron uptake.	J Biol Chem	2000	10744769
Trans-acting regulatory variation (dye swap)	90	Investigation of trans-acting regulatory variation using laboratory (BY) and wild (RM) strains and 86 F1 haploid cross segregants	Yvert G	"Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, Mackelprang R, Kruglyak L"	Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors.	Nat Genet	2003	12897782
Trans-acting regulatory variation	90	Investigation of trans-acting regulatory variation using laboratory (BY) and wild (RM) strains and 86 F1 haploid cross segregants	Yvert G	"Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, Mackelprang R, Kruglyak L"	Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors.	Nat Genet	2003	12897782
Pseudohyphal Growth	26	"Wild-type or isogenic fkh1 fkh2 cells (GZ45-17a) were synchronized with -factor, released, and sampled through two cell cycles. Relative mRNA abundance was analysed by competitive microarray hybridization."	Zhu G	"Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B"	Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth.	Nature	2000	10894548