SGD.SL: Interaction data from the Saccharomyces Genome Database
In SLGI: Synthetic Lethal Genetic Interaction

Description Usage Format Details Author(s) Source Examples

The Saccharomyces Genome Database (SGD) provides, for download a table listing all known interactions in yeast. This table was downloaded on Jan 25, 2007 and three subsets were extracted. The synthetic lethal interactions, SGD.SL, the synthetic grow defect interactions, SGD.SynGrowthDefect and the synthetic rescue interactions, SGD.SynRescue. No other processing has been done.

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  data(SGD.SL)
  data(SGD.SynRescue)
  data(SGD.SynGrowthDefect)

Each data set is a data frame with the following 7 variables.

V1: Factor, indicating the type of data.
V2: Factor describing the interaction, in particular naming bait and prey and interactors.
V3: Factor indicating whether the cells were viable.
V4: Factor which is always NA for these data.
V5: Factor naming the reference for the interaction.
V6: Factor with levels indicating the PubMed ID for the publication in V5.
V7: Factor with level BioGRID, probably indicating the source.

SGD says this about the file:

Contains interaction data.  Tab-separated columns are:
1) interaction_type (mandatory)
2) genes involved and their mutation type, in the format: ORF
(mutation_type, action), with multiples separated by a | 
3) phenotype (optional, multiples separated by |)
4) description (optional)
5) citation (multiples separated by |)
6) PubMed ID (optional, multiples separated by |)

This file is updated weekly.

Z. Jiang

The file can be downloaded from, ftp://genome-ftp.stanford.edu/pub/yeast/literature_curation.

1	data(SGD.SL)

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