\HeaderA{GiaeverPheno}{List of fitness defect score generated from Giaever et al 2002}{GiaeverPheno}
\aliasA{GiaeverExpCdt}{GiaeverPheno}{GiaeverExpCdt}
\aliasA{GiaeverGene}{GiaeverPheno}{GiaeverGene}
\aliasA{Giaeverresult}{GiaeverPheno}{Giaeverresult}
\keyword{datasets}{GiaeverPheno}
\begin{Description}\relax
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.
\end{Description}
\begin{Usage}
\begin{verbatim}
data(GiaeverPheno)
data(GiaeverGene)
data(GiaeverExpCdt)
\end{verbatim}
\end{Usage}
\begin{Format}\relax
\code{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).

\code{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 \emph{Saccharomyces Genome Database}.

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

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

\code{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 \code{CoHyperGParams-class}
for more details) and the \code{complexStatus} function.
\end{Format}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{Source}\relax
Giaever et al (2002), supplementary information:
\url{http://genomics.lbl.gov/YeastFitnessData/websitefiles/cel_index.html}
Saccharomyces Genome Database (last update 03/17/06):
\url{http://www.yeastgenome.org/}
\end{Source}
\begin{References}\relax
Giaever G et al (2002) Functional profiling of the Saccharomyces cerevisiae
genome. Nature. 418(6896):387-91. PMID: 12140549
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(GiaeverPheno)
data(GiaeverExpCdt)
data(GiaeverGene)
\end{ExampleCode}
\end{Examples}

