Download yeast datasets

This page contains links to downloads of various published large-scale yeast datasets. Note that this is not nearly an exhaustive list. A short-term goal is to improve upon our collection of yeast datasets, so check back frequently for new data, and let us know if there are datasets we should add. Our longer term goal is to incorporate all these data within the SGD Lite database. The following is the set of directories and subdirectories that contain files for download. ArrayExpress has kindly provided MAGE-ML files for the yeast data sets that had been submitted to their repository. These are within the mage_ml/ directory and are also listed below.

Expression

Contains various types of large-scale expression data. Files available for download are listed below. pcl files are preclustered files, while cdt files are clustered, complete data files. For more info on these file formats, see the SMD file format documentation page.

DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278(5338):680-6: MAGE-ML | pcl

Cho RJ et al (1998) Genome-Wide transcriptional analysis of the mitotic cell cycle. Mol.Cell 2(1):65-73: txt | Web supplement.

Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9(12):3273-97: pcl

Galitski T, Saldanha AJ, Styles CA, Lander ES, Fink GR (1999) Ploidy regulation of gene expression. Science 285(5425):251-4: pcl | cdt

Ferea TL, Botstein D, Brown PO, Rosenzweig RF (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A 96(17):9721-6
pcl

Wyrick JJ, Holstege FC, Jennings EG, Causton HC, Shore D, Grunstein M, Lander ES, Young RA (1999) Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402(6760):418-21: pcl

Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO (2001) Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell 12(10):2987-3003: pcl | cdt

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 (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287(5454):873-80: pcl

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 (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287(5454):873-80: pcl

Ogawa N, DeRisi J, Brown PO (2000) New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell 11(12):4309-21: pcl

Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11(12):4241-57: pcl

Travers KJ, Patil CK, Wodicka L, Lockhart DJ, Weissman JS, Walter P (2000) Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101(3):249-58: pcl

Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS (2002) Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J Biol Chem 277(34):31079-88: MAGE-ML | pcl

Preiss T, Baron-Benhamou J, Ansorge W, Hentze MW. (2003) Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nat Struct Biol. 10(12):1039-47: MAGE-ML

van de Peppel J, Kemmeren P, van Bakel H, Radonjic M, van Leenen D, Holstege FC. (2003) Monitoring global messenger RNA changes in externally controlled microarray experiments. EMBO Rep. 4(4):387-93: MAGE-ML

Meneghini MD, Wu M, Madhani HD (2003) Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112(5):725-736 and Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, Link AJ, Madhani HD, Rine J (2004) A Protein Complex Containing the Conserved Swi2/Snf2-Related ATPase Swr1p Deposits Histone Variant H2A.Z into Euchromatin. PLoS Biol. 2(5):E131: pcl | cdt

Sollier J, Lin W, Soustelle C, Suhre K, Nicolas A, Geli V, De La Roche Saint-Andre C. (2004) Set1 is required for meiotic S-phase onset, double-strand break formation and middle gene expression. EMBO J.23(9):1957-67: MAGE-ML

Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C (2004) ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303(5656):343-8: pcl | cdt

SAGE

Data generated by Velculescu et al., (1997) Cell 88:243-251 should be downloaded from the main SGD site because the chromosomal coordinates of the SAGE tags are periodically updated when there are sequence changes in SGD.

Genome wide chromatin IP

Ren B, et al. (2000) Genome Wide Location and Function of DNA-Binding Proteins. Science 290:2306-9
Web supplement with data download

Lieb JD, et al. (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28(4):327-34
Web supplement with data download

Iyer VR, et al. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409(6819):533-8
Web supplement with data download

Damelin M, et al. (2002) The Genome-Wide Localization of Rsc9, a Component of the RSC Chromatin-Remodeling Complex, Changes in Response to Stress. Mol. Cell 9:563-73
Web supplement with data download

Lee et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 298(5594):799-804. MAGE-ML

Nagy PL, et al. (2003) Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. Proc Natl Acad Sci U S A 100(11):6364-6369
Web supplement with data download

Harbison et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
Web supplement with data download
Also available for download through the SGD Lite package

Other types of microarray experiments

Peng et al (2003) A panoramic view of yeast noncoding RNA processing. Cell 113(7):919-33. MAGE-ML

Interactions

tong2004.tab:
Contains the genetic interaction data from Tong et al. 2004 Global Mapping of the Yeast Genetic Interaction Network. Science. 303(5659):808-813. The file consists of the following tab-separated columns:
- Interaction pairs and the allele used, in the format:
  ORF (mutation_type)|ORF (mutation_type)
- Phenotype (inviable or slow growth)
- Note
- Citation (multiples separated by |)
- PubMed ID (multiples separated by |)
Note that while this dataset is based on the Tong et al 2004 paper, the authors also provided some additional references where the genetic interactions were confirmed.

ms_interactions.txt
y2h_hits.txt
Hazbun et al Assigning Function to Yeast Proteins by Integration of Technologies. Molecular Cell, Vol 12, 1353-1365. The ms_interactions.txt file contains the predicted mass spec interactions, and the y2h_hits.txt contains the yeast two-hybrid data described in the paper. Thanks to Michael Riffle for providing these data; for a list of complexes and more information, see the authors' Yeast Resource Center (YRC) web page.

GRID (downloads), DIP (downloads), and BIND (downloads) are databases with extensive interaction data; you can go to their web sites to find more interaction data. We hope to soon provide yeast data files from various interaction databases on this site.

Localization

OSheaLocalization.WeissmanAbundance.tab:
Contains the geneome wide protein localization data from Huh et al. (2003), Nature 425:686-691 and protein abundance data from Ghaemmaghami et al. (2003), Nature 425:737-741. More information about this dataset is available here.

Other sources of downloadable localization data are:

Yale Genome Analysis Center download page
Gene Ontology (GO) Cellular Component annotations: all cellular component annotations can be parsed from the gene_association.sgd.gz file in the above directory. In addition, the go_protein_complex.tab file contains gene products mapped to macromolecular complex terms.

Phenotypes

Mitochondrial-related phenotypes

The following files contain data from Steinmetz LM, et al. (2002) Systematic screen for human disease genes in yeast. Nat Genet 31(4):400-4. Go to their project web site for more information.

Cell size control

The following files contain data from Jorgensen P. et al, (2002) Systematic Identification of Pathways That Couple Cell Growth and Division in Yeast 297:395-400. Go to their supplemental web site for more information. The files below were downloaded from their supplemental web site.

haploidSize.xls (15.9 MB): excel file that contains hierarchical clustering of cell size distributions of 4812 viable haploid deletion strains (see Fig. 1B of paper).
heterozygoteSize.xls (4.3 MB): excel file that contains hierarchical clustering of cell size distributions of 1142 diploid strains heterozygous for deletion of an essential gene (see Fig. 1B of paper).
jorgensenMicroarrayFig4A.xls (3.5 MB): excel file that contains data from the microarray experiment that examined Sfp1-dependent expression (see Fig. 4A of paper).

Footprinting

Data from the large-scale genetic footprinting study by Dunn et al:

growthScores.tab:
Contains phenotypic results for all the ORFs tested. Columns are:
- ORF name
- growth after 20 generations in YPD (2% glucose)
- growth after 60 generations in YPD (2% glucose)
- growth in minimal (YNB) medium (2% glucose)
- growth in YPD (2% glucose) plus 0.9 M NaCl
- growth in YP plus 2% lactate
'Ess' indicates that the gene is essential for growth under the condition tested. 'Non' indicates that the gene is not essential. A number indicates that the gene when mutated exhibits an intermediate phenotype; the number is the relative growth score. 'ND' indicates that no data are available. For example, the following row:
```
YAR020C 0.8     0.8     Non     0.8     Non
```
indicates that YAR020C has an intermediate defect after 20 generations and 60 generations on YPD, is non-essential for growth in minimal medium, has an intermediate defect on NaCl, and is non-essential for growth on lactate.

rawScores.tab:
Contains the raw ratio scores for all the ORFs tested. Columns are:
- ORF name
- growth after 20 generations in YPD (2% glucose)
- growth after 60 generations in YPD (2% glucose)
- growth in minimal (YNB) medium (2% glucose)
- growth in YPD (2% glucose) plus 0.9 M NaCl
- growth in YP plus 2% lactate

The following files indicate, for each condition tested, the probability cutoffs for mutations that cause severe, intermediate, or no growth defects. The probability is in the 2nd column, and asteriks (*) in the 3rd column indicate the cutoffs.

rawNaCl.txt

raw20Gen.txt

raw60Gen.txt

rawYNB.txt

rawLactate.txt

Results from the Saccharomyces Genome Deletion Project

The Deletion Consortium provides a downloads page that contains several data files, including the list of essential ORFs, overlapping ORFs, and much more.

All phenotype data in SGD

You can get all the phenotype data in the main SGD database by downloading the phenotypes.tab in this ftp directory. Be sure to read the README file in the same directory for important information about these data.

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Send questions, suggestions, and comments to: sgdlite@genomics.princeton.edu