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 1.6.0 Index]