Giaever: List of fitness defect score generated from Giaever et al...

In PCpheno: Phenotypes and cellular organizational units

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)

PCpheno documentation built on Nov. 8, 2020, 5:10 p.m.