GiaeverPheno {PCpheno}R Documentation

List of fitness defect score generated from Giaever et al 2002

Description

Giaever et al (2002) create a collection of gene-deletion mutants to determine genes that contribute to a particular phenotype in specific environmental conditions. This list is generated from a fitness analysis under six different experimental conditions.

Usage

data(GiaeverPheno)
data(GiaeverGene)
data(GiaeverExpCdt)

Format

GiaeverPheno is a list with 31 elements. The name of each element is a experimental condition (see details). The value of each element are the fitness defect scores for the genes sensitive to the experimental condition, as defined by Giaever et al (2002).

GiaeverGene Vector of the systematic gene names of the 5898 tested genes. Note that some updates have been made for the list to be consistent with Saccharomyces Genome Database.

GiaeverExpCdt is a 3 columns dataframe with fileID from which the data were extracted, the generation time (growth time) and the condition (media).

gen.
generations
rep.
replicate
ypg5a,ypg5b
yeast/peptone/galactose 5 gen. rep. a and b ==> carbone source
ypg15a ypg15b
yeast/peptone/galactose 15 gen. rep. a and b ==> carbone source
sorbitol5a sorbitol5b
1.5M Sorbitol 5 gen. rep. a and b ==> sugar, osmotic stress
sorbitol20a sorbitol15b
1.5M Sorbitol 20 and 15 gen. rep. a and b respectively==> sugar, osmotic stress
NaCl5a NaCl5b
1M NaCl 5 gen. rep. a and b ==> salt, osmotic stress
NaCl15a NaCl15b
1M NaCl 15 gen. rep. a and b ==> salt, osmotic stress
lysM5a lysM5b
lysine minus 5 gen. rep. a and b ==> lack of required AA
thM5a
threonine minus 5 gen. rep. a ==> lack of required AA
trpM5a trpM5b
tritophanee minus 5 gen. rep. a ==> lack of required AA
minimalPlus5a minimalPlus5b
minimal + histidine/leuvine/uracile 5 gen. rep. a and b
minimalPlus15a minimalPlus15b
minimal + histidine/leuvine/uracile 15 gen. rep. a and b
minimalC5a minimalC5b
minimal complete 5 gen. rep. a and b
nystatin5a nystatin5b
Nystatin 5 gen. rep. a and b ==> antifungal drug
nystatin15a nystatin15b
Nystatin 5 gen. rep. a and b ==> antifungal drug
pH8g5a pH8g5b
pH 8 5 gen. rep. a and b ==> alkali stress
pH8g15a pH8g20b
pH 8 15 and 20 gen. rep. a and b respectively ==> alkali stress

Note: in their study they confound the 15 and 20 generations.

Giaeverresult is a data.frame that summaryzes the number of sensitive genes per condition, how many of those genes are present in the ScISI interactome and the associated p-value. This is the result of applying a Hypergeometric test (see CoHyperGParams-class for more details) and the complexStatus function.

Author(s)

N. LeMeur

Source

Giaever et al (2002), supplementary information: http://genomics.lbl.gov/YeastFitnessData/websitefiles/cel_index.html Saccharomyces Genome Database (last update 03/17/06): http://www.yeastgenome.org/

References

Giaever G et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418(6896):387-91. PMID: 12140549

Examples

data(GiaeverPheno)
data(GiaeverExpCdt)
data(GiaeverGene)

[Package PCpheno version 1.4.1 Index]