yeast {JMDplots}

R Documentation

Composition, localization, and abundances of proteins in yeast

Description

Retrieve the amino acid compositions of one or more proteins from Saccharomyces cerevisiae and get localizations and abundances reported by the YeastGFP project or locations from the SGD gene associations.

Usage

  yeast.aa(protein = NULL)
  yeastgfp(location, exclusive = TRUE)
  yeast.ZC(location)

Arguments

protein	character, name of protein
location	character, name (yeastgpf) or one-letter code (yeast.ZC) for subcellular location
exclusive	logical, report only proteins exclusively localized to a compartment?

Details

yeast.aa retrieves the amino acid composition(s) of the indicated proteins in Saccharomyces cerevisiae. The calculation depends on the data file extdata/organisms/Sce.csv.xz, which contains the amino acid compositions of the proteins. The protein argument should be a vector or a list of vectors of one or more SGD IDs, Open Reading Frame (ORF) or gene names that are found in these files. The output data frame contains rows with NA compositions for names that are not matched. If protein is NULL, all available proteins are returned except those with NA amino acid composition.

yeastgfp returns the identities and abundances of proteins with the requested subcellular localization(s) (specified in location) using data from the YeastGFP project that is stored in extdata/abundance/yeastgfp.csv.xz. If exclusive is FALSE, the function grabs all proteins that are localized to a compartment even if they are also localized to other compartments. If exclusive is TRUE (the default), only those proteins that are localized exclusively to the requested compartments are identified, unless there are no such proteins, then the non-exclusive localizations are used (applies to the ‘⁠bud⁠’ localization).

yeast.ZC returns the ZC of proteins in the subcellular location identified by the one-letter abbreviation. This abbreviation identifies a “Cellular Component” in the Gene Ontology and the associatied proteins (see aoscp).

Value

For yeast.aa, a data frame, or list of data frames, containing the amino acid composition(s) of the specified protein(s) in the format of thermo$protein.

For yeastgfp, a list with elements named protein (names of proteins) and abundance (counts or concentrations without any conversion from the units in the data file). If location is NULL, yeastgfp returns the names of all known locations, and if the length of location is >1, the protein and abundance values are lists of the results for each location.

References

Ghaemmaghami S, Huh W, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK and Weissman JS (2003) Global analysis of protein expression in yeast. Nature 425(6959), 737–741. doi:10.1038/nature02046

Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS and O'Shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425(6959), 686–691. doi:10.1038/nature02026

YeastGFP project. Yeast GFP Fusion Localization Database, http://yeastgfp.ucsf.edu; Current location: https://yeastgfp.yeastgenome.org

See Also

scsc

Examples

# The first few names in UniProt for "aminotransferase yeast"
genes <- c("AATC", "ARO8", "BCA1", "AMPL", "BCA2", "ARO9")
# the corresponding ORF names
ORF <- c("YLR027C", "YGL202W", "YHR208W", "YKL103C", "YJR148W", "YHR137W")
# We only match two of them by gene name, but all by ORF name
aa <- yeast.aa(genes)
aa <- yeast.aa(ORF)
# What are their formulas and average oxidation states of carbon
protein.formula(aa)
ZC(protein.formula(aa))

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