Resources page


Sources from the Saccharomyces Genome Database (SGD).

These source data are taken from downloads.yeastgenome.org/curation/: that include the following and other files.
These raw data can be downloaded directly by clicking the following links

From the SGD literature/ folder:
biochemical_pathways.tab
gene_literature.tab
go_protein_complex_slim.tab
go_slim_mapping.tab
go_terms.tab
interaction_data.tab
phenotype_data.tab
From the SGD chromosomal_feature folder:
SGD_features.tab
chromosome_length.tab
From the SGD calculated_protein_info folder:
protein_properties.tab


Related Publications

Screens of the heterozygous diploid deletion library using the 96-well plate method

1. Baetz K, McHardy L, Gable K, Tarling T, Reberioux D, Bryan J, Andersen RJ, Dunn T, Hieter P, Roberge M: Yeast genome-wide drug-induced haploinsufficiency screen to determine drug mode of action. Proc Natl Acad Sci U S A. 2004, 101(13):4525-4530. link
2. Botet J, Mateos L, Revuelta JL, Santos MA: A chemogenomic screening of sulfanilamide-hypersensitive Saccharomyces cerevisiae mutants uncovers ABZ2, the gene encoding a fungal aminodeoxychorismate lyase. Eukaryot Cell. 2007, 6(11):2102-2111. link
3. Choy JS, O'Toole E, Schuster BM, Crisp MJ, Karpova TS, McNally JG, Winey M, Gardner MK, Basrai MA: Genome-wide haploinsufficiency screen reveals a novel role for gamma-TuSC in spindle organization and genome stability. Mol Biol Cell. 2013, 24(17):2753-2763. link
4. de Clare M, Oliver SG: Copy-number variation of cancer-gene orthologs is sufficient to induce cancer-like symptoms in Saccharomyces cerevisiae. BMC Biol. 2013, 11:24. link
5. Jarolim S, Ayer A, Pillay B, Gee AC, Phrakaysone A, Perrone GG, Breitenbach M, Dawes IW: Saccharomyces cerevisiae genes involved in survival of heat shock. G3 (Bethesda). 2013, 3(12):2321-2333. link
6. Jorgensen P, Nishikawa JL, Breitkreutz BJ, Tyers M: Systematic identification of pathways that couple cell growth and division in yeast. Science. 2002, 297(5580):395-400. link
7. Lain S, Hollick JJ, Campbell J, Staples OD, Higgins M, Aoubala M, McCarthy A, Appleyard V, Murray KE, Baker L et al: Discovery, in vivo activity, and mechanism of action of a small-molecule p53 activator. Cancer Cell. 2008, 13(5):454-463. link
8. Lis M, Bhatt S, Schoenly NE, Lee AY, Nislow C, Bobek LA: Chemical genomic screening of a Saccharomyces cerevisiae genomewide mutant collection reveals genes required for defense against four antimicrobial peptides derived from proteins found in human saliva. Antimicrob Agents Chemother. 2013, 57(2):840-847. link
9. Okada N, Ogawa J, Shima J: Comprehensive analysis of genes involved in the oxidative stress tolerance using yeast heterozygous deletion collection. FEMS Yeast Res. 2014, 14(3):425-434. link
10. Pan X, Reissman S, Douglas NR, Huang Z, Yuan DS, Wang X, McCaffery JM, Frydman J, Boeke JD: Trivalent arsenic inhibits the functions of chaperonin complex. Genetics. 2010, 186(2):725-734. link
11. Prescott TA, Panaretou B, Veitch NC, Simmonds MS: A yeast chemical genetics approach identifies the compound 3,4,5-trimethoxybenzyl isothiocyanate as a calcineurin inhibitor. FEBS Lett. 2014, 588(3):455-458. link
12. Shim JS, Rao R, Beebe K, Neckers L, Han I, Nahta R, Liu JO: Selective inhibition of HER2-positive breast cancer cells by the HIV protease inhibitor nelfinavir. J Natl Cancer Inst. 2012, 104(20):1576-1590. link
13. Shimada K, Filipuzzi I, Stahl M, Helliwell SB, Studer C, Hoepfner D, Seeber A, Loewith R, Movva NR, Gasser SM: TORC2 signaling pathway guarantees genome stability in the face of DNA strand breaks. Mol Cell. 2013, 51(6):829-839. link
14. Sinha H, David L, Pascon RC, Clauder-Munster S, Krishnakumar S, Nguyen M, Shi G, Dean J, Davis RW, Oefner PJ et al: Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast. Genetics. 2008, 180(3):1661-1670. link
15. Strome ED, Wu X, Kimmel M, Plon SE: Heterozygous screen in Saccharomyces cerevisiae identifies dosage-sensitive genes that affect chromosome stability. Genetics. 2008, 178(3):1193-1207. link
16. Teixeira MC, Raposo LR, Mira NP, Lourenco AB, Sa-Correia I: Genome-wide identification of Saccharomyces cerevisiae genes required for maximal tolerance to ethanol. Appl Environ Microbiol. 2009, 75(18):5761-5772. link
17. Xie MW, Jin F, Hwang H, Hwang S, Anand V, Duncan MC, Huang J: Insights into TOR function and rapamycin response: chemical genomic profiling by using a high-density cell array method. Proc Natl Acad Sci U S A. 2005, 102(20):7215-7220. link

Screens of the haploid deletion library using the 96-well plate method

1. Svensson JP, Pesudo LQ, Fry RC, Adeleye YA, Carmichael P, Samson LD: Genomic phenotyping of the essential and non-essential yeast genome detects novel pathways for alkylation resistance. BMC Syst Biol. 2011, 5:157. link


Download database information

Most of the gene lists use for this database were taken fron the SGD files phenotype_data.tab and gene_literature.tab. Additional data was taken directly from the original publications. A compilation of all of these data can be downloaded using the button below as a TAB seperated text file.



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Data Source Publication Phenotype Gene Name Feature Name SGD Feature qualifier SGD ID PubMed ID Gene length (bp) Process (GO slim) Function (GO slim) Component (GO slim) SGD Description
original_article Alamgir M, et al. (2008) Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis. BMC Genomics 9:583 sensitive to both paromomycin and calcofluor white "paromomycin (13 mg/ml), calcofluor white (40 _g/ml)" AHP1 YLR109W Verified S000004099 19055778 530 response to chemical, response to oxidative stress oxidoreductase activity cytoplasm, membrane, plasma membrane Thiol-specific peroxiredoxin; reduces hydroperoxides to protect against oxidative damage; function in vivo requires covalent conjugation to Urm1p
original_article Alamgir M, et al. (2008) Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis. BMC Genomics 9:583 sensitive to both paromomycin and calcofluor white "paromomycin (13 mg/ml), calcofluor white (40 _g/ml)" ATP4 YPL078C Verified S000005999 19055778 734 ion transport, nucleobase-containing small molecule metabolic process, protein complex biogenesis, transmembrane transport ATPase activity, hydrolase activity, transmembrane transporter activity cytoplasm, membrane, mitochondrial envelope, mitochondrion Subunit b of the stator stalk of mitochondrial F1F0 ATP synthase; ATP synthase is a large, evolutionarily conserved enzyme complex required for ATP synthesis; contributes to the oligomerizatio......

Other usefull links and tools

GO tools

Gene Ontology annotations are commonly used to help interprete genome-wide experiments such as deletion library screen data, on this site the simplified GO slim terms were used. The following sites provide tools for a more complete analyses of GO terms

The Gene Ontology Consortium GO Consortium
Tools at SGD goSlimMapper
Gene Ontology enRIchment anaLysis and visuaLizAtion tool gorilla
Functional Specification yeast gene names funspec

Deletion Project web pages

The Saccharomyces Deletion Library ia an almost complete set of yeast deletion strains. Screening of the phenotypic response of these mutants is an important tool to identify gene function and cellular pathways.The following sites provide more information on this resource.

The Saccharomyces Genome Deletion Project web page Stanford
Yeast Knockout Collection Dharmacon

Source file from Project web page;
Homozygous Diploid list Strain list
ORFs not available list Strain list
Essential ORFs list Strain list

Related Deletion Collections

Mulleder, M., Capuano, F., Pir, P., Christen, S., Sauer, U., Oliver, S. G., & Ralser, M: A prototrophic deletion mutant collection for yeast metabolomics and systems biology. Nature Biotechnology. 2012, 30(12), 1176-1178. link

Useful Sites

GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Shared genes downloded from the "ENTER YOUR GENESET" tool can be cut and pasted into GeneMANIA to see how highly connected they are. Other genelists from the DeLiTo tools that are comma seperated need to be reformated to replace the commas with paragraph returns before they can be used at GeneMANIA.