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,
synthetic grow defect interactions,
SGD.SynGrowthDefect and the
synthetic rescue interactions,
SGD.SynRescue. No other processing
has been done.
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Each data set is a data frame with the following 7 variables.
Factor, indicating the type of data.
Factor describing the interaction, in particular naming bait and prey and interactors.
Factor indicating whether the cells were viable.
Factor which is always NA for these data.
Factor naming the reference for the interaction.
Factor with levels indicating the PubMed ID for the publication in V5.
Factor with level
indicating the source.
SGD says this about the file:
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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.
The file can be downloaded from, ftp://genome-ftp.stanford.edu/pub/yeast/literature_curation.
Loading required package: ScISI Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: RpsiXML Loading required package: annotate Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode Loading required package: RBGL Loading required package: hypergraph No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML' No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML' Attaching package: 'RpsiXML' The following object is masked from 'package:IRanges': members Loading required package: apComplex Loading required package: lattice No methods found in package 'BiocGenerics' for request: 'plot' when loading 'SLGI'
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