\HeaderA{OsterbergRaw}{Data from Osterberg at al. 2006}{OsterbergRaw}
\keyword{datasets}{OsterbergRaw}
\begin{Description}\relax
Osterberg at al. (2006) report growth phenotypes in yeast for a strain
collection over-expression \textasciitilde{}600 C-terminal tagged integral membrane
proteins growth both under normal and three different stress
conditions.
\end{Description}
\begin{Usage}
\begin{verbatim}
data(OsterbergRaw)
\end{verbatim}
\end{Usage}
\begin{Format}\relax
\code{OsterbergRaw} is a 17 columns dataframe.

\describe{ 
\item[SYSTEMATIC] Systematic gene names of the studied membrane protein
\item[COMMUN] Commun gene names of the studied membrane protein
\item[TMHMM.C] The topology predicted by TMHMM (TransMembrane
prediction using Hidden Markov Models)
using the experimentally assigned C-terminal location for the protein as a
constraint. The topology is represented in the format Location of
N-terminus TMhelices Location of C-terminus (i and o stand for in
and out respectively)
\item[WesternBlot] Protein expression levels (arbitrary units),
estimated from the band intensity and normalized to the internal
standard on each Western blot.
\item[Bands] Proteins detected as two distinct bands with different
molecular mass on the Western blot analysis. category 1 indicates
that both bands were insensitive to Endo H digestion, 2 indicates
the higher molecular mass was shifted down upon Endo H digestion
on SDS/PAGE and one  band was predominant compared to the other,
and 3 indicates that a higher molecular mass band shifted down
upon Endo H digestion on SDS/PAGE and both bands were equal
intensity on Western blot
\item[Toxicity] Toxicity index from Spoko et al. (2006). The index
varies between 1 and 5, where 1 means the strain is dead, and 5
indicates no difference in growth rate compared with the wild type strain.
\item[sign.norm] Over-expression strains that show a significant
(P\textless{}0.001) growth rate phenotype (LSCrate) in synthetic defined
medium conditions (Warringer et al., 2003). An average of two
replicates is given. Strains that do not show a significant
difference in doubling time compared with the wild-type strain are
indicated by 0.
\item[all.norm] Phenotypes (significant or not) of over-expression
strains (LSCrate) in synthetic defined medium conditions
(Warringer et al., 2003). An average of two replicates is given.
\item[sign.NaCl] Over-expression strains that show a significant
(P\textless{}0.001) growth rate phenotype (LPIrate) in NaCl. An average of two
replicates is given. Strains that do not show a significant
difference in doubling time compared with the wild-type strain
under NACL stress are indicated by 0.
\item[all.NaCl.LSC] Phenotypes (significant or not) of over-expression
strains (LSCrate) in NaCl (Warringer et al., 2003).
An average of two replicates is given.
\item[all.NaCl.LPI] Phenotypes (significant or not) of over-expression
strains (LPIrate) in NaCl (Warringer et al., 2003).
An average of two replicates is given.
\item[sign.caff] Over-expression strains that show a significant
(P\textless{}0.001) growth rate phenotype (LPIrate) in caffeine. An average of two
replicates is given. Strains that do not show a significant
difference in doubling time compared with the wild-type strain
under caffeine stress are indicated by 0.
\item[all.caff.LSC] Phenotypes (significant or not) of over-expression
strains (LSCrate) in caffeine (Warringer et al., 2003).
An average of two replicates is given
\item[all.caff.LPI] Phenotypes (significant or not) of over-expression
strains (LPIrate) in caffeine (Warringer et al., 2003).
An average of two replicates is given.
\item[sign.paraq.] Over-expression strains that show a significant
(P\textless{}0.001) growth rate phenotype (LPIrate) in paraquat. An average of two
replicates is given. Strains that do not show a significant
difference in doubling time compared with the wild-type strain
under paraquat stress are indicated by 0.
\item[all.paraq.LSC] Phenotypes (significant or not) of overexpression
strains (LSCrate) in paraquat (Warringer et al., 2003).
An average of two replicates is given.
\item[all.paraq.LPI] Phenotypes (significant or not) of overexpression
strains (LPIrate) in paraquat (Warringer et al., 2003).
An average of two replicates is given.
}
\end{Format}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{Source}\relax
Osterberg et al (2006), supplementary information:
\url{http://www.pnas.org/content/vol0/issue2006/images/data/0604078103/DC1/04078Table1.xls}
or  \url{ftp://genome-ftp.stanford.edu/pub/yeast/systematic_results/phenotypes}
\end{Source}
\begin{References}\relax
Osterberg M, Kim H, Warringer J, Melen K, Blomberg A, von Heijne
G. (2006) Phenotypic effects of membrane protein overexpression in Saccharomyces
cerevisiae. PNAS. 103(30):11148-53. PMID: 16847257
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(OsterbergRaw)
str(OsterbergRaw)

\end{ExampleCode}
\end{Examples}

