ExpressDB is a collection of yeast RNA expression datasets created at the Church Labs and at other laboratories prior to 2002.
The page link shown in the Downloads column for these data sets is a link to a page from which you can download data files and information files associated with that data set. The here links in the More Info column are links to pages that provide a lot more information about each data set, including citations and in some cases links to web pages provided by the citation authors
For historical information: general information about ExpressDB
| Data Set | Description | Downloads | More Info |
|---|---|---|---|
| Barak Cohen yap1 and yap2 knockouts with peroxide and cadmium added | Summaries of multiple gene chip experiments, wt, yap1 and yap2 knockouts and combinations with various treatments | page | here |
| Butow study of genome wide responses to mitochondrial dysfunction | Signed geometric means of log base 10 ratios of replicated microarray hybridizations | page | here |
| Cho: mitotic cell cycle | 17 time points of expression data for synchronized yeast cells | file | here |
| Chu_spo: sporulation | 7 times points of mRNA expression data for YSC328: 0.5, 2, 5, 6, 7, 9, and 11.5 hours. 3 time points for ndt80-deficient YSC328: 0, 2, and 6 hours. gal-ndt80 induced 3 hours prior to harvesting. | file | here |
| Der_diaux: diauxic shift data | expression levels during metabolic shift from fermentation to respiration | page | here |
| Der_tup: tup1 deletion data | expression levels as affected by deletion of transcriptional co-repressor TUP1 | page | here |
| Der_yap: YAP1 overexpression data | expression levels as affected by overexpression of DNA-binding transcription factor YAP1 | page | here |
| Eis: Eisen clustering data | expression levels 14 new conditions and data from sources DeRisi97-Chu98, Cho98, and Spellman98 | file | here |
| Genomic Expression Programs in Response to Environmental Changes | Expression Time Series following treatment with a variety of stresses, including temperature shifts, osmolarity, esposure to peroxide, menadione, diamide, DTT, amino acid starvation, and nitrogen depletion. | file | here |
| Hol_gcn5_del: GCN5 deletion data | expression levels as affected by deletion of GCN5 | page | here |
| Hol_kin28_ts: temperature sensitive KIN28 mutant data | expression levels as affected by temp sensitive mutation of KIN28 | page | here |
| Hol_med6_ts: temperature sensitive MED6 mutant data | expression levels as affected by temp sensitive mutation of MED6 | file | here |
| Hol_rpb1_ts: temperature sensitive RPB1 mutant data | expression levels as affected by temp sensitive mutation of RPB1 (SGD name rpo21) | page | here |
| Hol_srb10_inact: SRB10 inactive mutation data | expression levels as affected by catalytically inactive point mutation of SRB10 (SGD name ssn3) | file | here |
| Hol_srb4_ts: temperature sensitive SRB4 mutant data | expression levels as affected by temp sensitive mutation of SRB4 | page | here |
| Hol_srb5_del: SRB5 deletion data | expression levels as affected by deletion of SRB5 | page | here |
| Hol_swi2_inact: swi2 inactive mutation data | expression levels as affected by catalytically inactive point mutation of swi2 (SGD name snf2) | page | here |
| Hol_taf145_ts: temperature sensitive TAF145 mutant data | expression levels as affected by temp sensitive mutation of TAF145 | page | here |
| Hol_taf17_ts: temperature sensitive TAF17 mutant data | expression levels as affected by temp sensitive mutation of TAF17 | file | here |
| Hol_tfa1_ts: temperature sensitive TFA1 mutant data | expression levels as affected by temp sensitive mutation of TFA1 | file | here |
| Jelinsky study of RPN4 links | Data showing coregulated DNA excision repair genes and protein degradation genes | file | here |
| Lopez and Baker study of gcr1 mutant | Data showing which genes have significantly lower expression for gcr1 mutants when grown on glucose | file | here |
| Mar: Rosetta datasets | 7 conditions (plus 4 repeats of wt, 1 of cna1cna2, 1 of his3) | page | here |
| Microarray Feature Names: Operon Oligos | This is a listing of oligo locations on the chips produced in the Church lab. | none | here |
| Microarray Feature Names: Research Genetics Intergenic Regions | This is a listing of names used for the Research Genetics intergenic names found on microarrays produced in the Church Lab so that a mapping to current SGD names and IDs can be made | page | here |
| Microarray Feature Names: Research Genetics ORF Regions | This is a listing of names used for the Research Genetics ORF names found on microarrays produced in the Church Lab so that a mapping to current SGD names and IDs can be made | page | here |
| Mye_gal: MED2 mutant galactose array | MED2 deletion strain effect when grown on galactose | none | here |
| Mye_heat: MED2 mutant heat shock array | MED2 deletion strain effect in heat shock experiment | none | here |
| Rosetta Compendium | data series corresponding to 300 diverse mutations and chemical treatments | page | here |
| Rosetta: Multiple MAPK Pathways | intensities, ratios, and P values for 56 series involving both wild type and MAPK pathway mutations | page | here |
| Rot: Glu/Gal/Mating type/Heat | absolute and relative expression levels for yeast cells grown in 4 conditions | page | here |
| SAGE transcript profiles from yeast grown on two different carbon sources | SAGE analysis of wild type and mutant cells grown on oleate for comparison with SAGE analysis of cells grown on glucose | none | here |
| Spe_alpha: Spellman alpha factor arrest time series data | 18 timepoints following removal of alpha factor added 120 minutes earlier | none | here |
| Spe_cdc15: Spellman cdc15 time series data | 25 data series from 23 timepoints following arrest of cdc15 temperature sensitive mutant | none | here |
| Spe_clb2: Spellman Clb2 experiments | CLB2 induction experiments | none | here |
| Spe_cln3: Spellman Cln3 experiments | CLN3 induction experiments | none | here |
| Spe_elut: Spellman elutriation experiment time series data | 14 timepoints following elutriation | none | here |
| Spe_summary: Spellman-processed summary of cell cycle series ratios | data from approximately 60 timepoints, with series following alpha factor arrest, elutriation, and arrest of cdc15 temperature sensitive mutant | page | here |
| Spe_wtgal: Spellman galactose addition control experiment | microarray measurements following addition of galactose | none | here |
| Vel: Log-phase + cell cycle arrested SAGE data | SAGE expression analysis of yeast transcriptome for log phase yeast cells, G1/S arrested cells, and G2/M arrested cells. | none | here |
| Yeast A kinase TPK1 mutant data | TPK1 expression profile from study of TPK1 (alternate name for YJL164C), TPK2 (alternate name for YPL203W), and TPK3 (YRL166C) mutants | file | here |
| Yeast A kinase TPK2 mutant data | TPK2 expression profile from study of TPK1 (alternate name for YJL164C), TPK2 (alternate name for YPL203W), and TPK3 (YRL166C) mutants | file | here |
| Yeast A kinase TPK3 mutant data | TPK3 expression profile from study of TPK1 (alternate name for YJL164C), TPK2 (alternate name for YPL203W), and TPK3 (YRL166C) mutants | file | here |
| Yeast Genome Expression Responses to Environmental Changes | Expression Time Series following treatment with heat, acid, alkali, hydrogen peroxide, salt, sorbital, and during diauxic shift | file | here |
| mRNA Decay Study | Data measuring the half-lives of each yeast mRNA after thermal inactivation of a temperature-sensitive RNA polymerase II. | none | here |
| snf/swi mutant expression analysis | microarray analysis of knockout mutants of snf and swi, two components of the Snf/Swi complex | page | here |
Please contact Wayne Rindone for more information, or with any questions, comments, or concerns.
Copyright (c) 2006 by Wayne Rindone and the President and Fellows of Harvard University