An Introduction to the Saccharomyces Genome Database (SGD)
The Saccharomyces Genome Database (SGD) is a well-established, key resource for researchers studying Saccharomyces cerevisiae. In addition to updating and maintaining the official genomic sequence of this highly studied organism, SGD provides integrated data regarding gene functions and phenotypes, which are extracted from the published literature. The vast amount and variety of data housed in the database can prove challenging to navigate for the first-time user. Therefore, this chapter serves as an introduction describing how to search the database in order to discover new information. We introduce the different types of pages on the website, and describe how to manipulate the tables and diagrams therein to display, download, or analyze the data using various SGD tools.
Key wordsSaccharomyces cerevisiae Genome database Phenotype Gene ontology Yeast
This work was supported by a U41 grant from the National Human Genome Research Institute at the US National Institutes of Health (HG001315) to the Saccharomyces Genome Database project. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health. Additional members of the SGD Project include: J. Michael Cherry, Gail Binkley, Felix Gondwe, Kalpana Karra, Kevin MacPherson, Stuart Miyasato, Travis Sheppard, Matt Simison, Marek Skrzypek, Shuai Weng, and Edith Wong.
- 1.Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: then and now. G3 (Bethesda) 4:389–398CrossRefGoogle Scholar
- 3.Cherry JM (2015) The Saccharomyces Genome Database: advanced searching methods and data mining. Cold Spring Harb Protoc. https://doi.org/10.1101/pdb.prot088906
- 6.Cherry JM (2015) The Saccharomyces Genome Database: gene product annotation of function, process, and component. Cold Spring Harb Protoc. https://doi.org/10.1101/pdb.prot088914
- 9.Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The Saccharomyces Genome Database variant viewer. Nucleic Acids Res 44(D1):D698–D702CrossRefPubMedGoogle Scholar
- 10.Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29CrossRefPubMedPubMedCentralGoogle Scholar
- 11.Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM (2010) Saccharomyces genome database provides mutant phenotype data. Nucleic Acids Res 38:D433–D436. https://doi.org/10.1093/nar/gkp917 CrossRefPubMedPubMedCentralGoogle Scholar