\HeaderA{DudleyPheno}{List of fitness defect score generated from Dudley et al 2005}{DudleyPheno}
\aliasA{Dudley}{DudleyPheno}{Dudley}
\aliasA{DudleyGenelist}{DudleyPheno}{DudleyGenelist}
\aliasA{DudleyPhenoFull}{DudleyPheno}{DudleyPhenoFull}
\aliasA{DudleyPhenoM}{DudleyPheno}{DudleyPhenoM}
\aliasA{Dudleyresult}{DudleyPheno}{Dudleyresult}
\aliasA{DudleySign}{DudleyPheno}{DudleySign}
\keyword{datasets}{DudleyPheno}
\begin{Description}\relax
Dudley et al (2005) 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 21 different experimental conditions.
\end{Description}
\begin{Usage}
\begin{verbatim}
data(DudleyGenelist)
data(DudleyPhenoFull)
data(DudleyPhenoM)
data(DudleySign)
\end{verbatim}
\end{Usage}
\begin{Format}\relax
\code{DudleyGenelist} is a character vector of length 814 genes.
\code{DudleyPhenoFull} is a dataframe of 814 genes by 23 elements.
The column contains the yeast gene name. The 22 remaining columns are
the experimental conditions (see details). The values obtained in
the different condition are the fitness defect scores for the
814 genes sensitive to the experimental condition, as defined
by Dudley et al (2005).
\code{DudleyPhenoM} is a 814 by 22 incidence matrix
with rownames corresponding to the genes names and
columns to an experimental condition. This matrix
contains a 1 in the (i,j) position if the i-th gene
is sensitive to the experimental condition of the j-th column;
it contains a 0 otherwise.

\describe{ 
\item[Yname] Yeast systematic gene name
\item[benomyl] 15ug/ml benomyl,microtubule function
\item[CaCl2] 0.7M calcium chloride, divalent cation
\item[CAD] 55uM Cadmium, heavy metal
\item[Caff] 2mg/ml Caffeine
\item[cyclohex] 0.18ug/ml cycloheximide, protein synthesis
\item[DTT] unknown
\item[EtOH] YPD + 6\% Ethanol
\item[FeLim] iron limited, nutrient limited condition
\item[HU] 11.4mg/ml Hydroxyurea, DNA replication and repair
\item[HygroB] 50ug/ml hygromycin B, aminoglycosides
\item[lowPO4] Low phosphate, nutrient limited condition
\item[MPA] 20ug/ml mycophenolic acid, transcriptional elongation
\item[NaCl] 1.2M sodium chloride, general stress condition
\item[Paraq] 1mM paraquat, oxidative stress
\item[pH3] Low pH, general stress condition
\item[rap] 0.1ug/ml rapamycin, protein synthesis
\item[Sorb] 1.2M sorbitol, general stress condition
\item[UV] 100J/m2 ultra-violet, DNA replication and repair
\item[YPGal] 2\% galactose, carbon source
\item[YPGly] 3\% glycerol, carbon source
\item[YPLac] 2\% lactate, carbon source
\item[YPRaff] 2\% raffinose, carbon source
}
\code{DudleySign} is a list of dataframe that summaryzes in which complexes
the gene related to the phenotype are found, the size of the
complexes 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.

\code{Dudleyresult} 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
Dudley et al (2005), supplementary information:
\url{http://arep.med.harvard.edu/pheno/default.htm}
\end{Source}
\begin{References}\relax
Aim\'ee Marie Dudley, Daniel Maarten Janse, Amos Tanay, Ron
Shamir and George McDonald Church. (2005).A global view of pleiotropy
and phenotypically derived gene function in yeast. \emph{Molecular Systems
Biology} doi:10.1038/msb4100004
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(DudleyPhenoFull)
data(DudleyPhenoM)
\end{ExampleCode}
\end{Examples}

