About

YeastPhenome.org is a collaborative project that aims at constructing a comprehensive compendium of systematic phenotypic data for budding yeast Saccharomyces cerevisiae.

Our goal is to collect, process and share in a standardized format the results of all genome-scale experiments that have examined the yeast deletion collection for any given phenotype under any given experimental condition.

In order to be included in the compendium, a study must meet all of the following criteria:

  1. use any current or past version of the Mat-a, Mat-alpha, homozygous diploid or heterozygous diploid deletion collection
  2. test at least 1,000 mutants
  3. record a quantitative (continuous) or qualitative (binary, discrete, categorical) phenotype (or the lack thereof) for all mutants
  4. report data on all of the tested mutants or just the most extreme/significant hits (studies that report an arbitrary subset of the hits based on biological interest are excluded)
  5. be described in a Pubmed-indexed journal article

Our primary source of data are the supplementary materials of the relevant publications. On top of that, many authors have contributed more complete and previously unpublished versions of their datasets (e.g., raw quantitative values from which the published hit list was derived). These datasets are explicitly flagged to emphasize their special status.

The individual datasets are available for download as soon as they are curated (e.g., see the green "Download all data" button for Bleackley MR~MacGillivray RT, 2011). The full compendium of all datasets will be accessible later on, as soon as we finalize the standardized nomenclature of phenotypes and experimental conditions.

Yeastphenome.org was created and is being maintained by:

  • Anastasia Baryshnikova (principal investigator, www.baryshnikova-lab.org)
  • Rose Oughtred (literature curator)
  • Christie Chang (literature curator)
  • Jennifer Rust (literature curator)
  • Brianna Richardson (curator, programmer)
  • Sven Heinicke (database and website support)
  • Fan Kang (database support)
  • Mark Schroeder (server support)

Data usage and citation policy

If you use yeast phenome data in a talk or a manuscript, please acknowledge the data source by citing the original publication from which the data is derived, as well as the yeast phenome database. The database should be cited as follows:

— Database of Systematic Phenotypic Screens in Yeast, www.yeastphenome.org, accessed on XXXX-XX-XX.

Current stats

  • Total publications: 325 (+ 26 for which data could not be recovered)
  • Publications with data loaded: 309 (95%)
  • Phenotypes with data loaded: 6,629
  • Environments with data loaded: 5,090
  • Total datasets: 15,680

Frequenty Asked Questions (FAQ)

Why is the drug name on this dataset different from the drug name in the paper?

What you see on this website is the ChEBI or the PubChem name of the drugs. Whenever possible, we associate chemical compounds with a ChEBI ID (preferentially) or a PubChem ID (if ChEBI ID was not available) and display, by default, their ChEBI or PubChem names, respectively. This sometimes results in an unusual name (e.g., the ChEBI name of rapamycin is sirolimus), but it greatly facilitates the consistency of the data. The original drug names (those used in the paper) are still available through search and will soon be displayed on the condition page.