OsterbergRaw {PCpheno} | R Documentation |
Data from Osterberg at al. 2006
Description
Osterberg at al. (2006) report growth phenotypes in yeast for a strain
collection over-expression ~600 C-terminal tagged integral membrane
proteins growth both under normal and three different stress
conditions.
Usage
data(OsterbergRaw)
Format
OsterbergRaw
is a 17 columns dataframe.
- SYSTEMATIC
- Systematic gene names of the studied membrane protein
- COMMUN
- Commun gene names of the studied membrane protein
- 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)
- WesternBlot
- Protein expression levels (arbitrary units),
estimated from the band intensity and normalized to the internal
standard on each Western blot.
- 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
- 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.
- sign.norm
- Over-expression strains that show a significant
(P<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.
- 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.
- sign.NaCl
- Over-expression strains that show a significant
(P<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.
- 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.
- 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.
- sign.caff
- Over-expression strains that show a significant
(P<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.
- 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
- 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.
- sign.paraq.
- Over-expression strains that show a significant
(P<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.
- all.paraq.LSC
- Phenotypes (significant or not) of overexpression
strains (LSCrate) in paraquat (Warringer et al., 2003).
An average of two replicates is given.
- all.paraq.LPI
- Phenotypes (significant or not) of overexpression
strains (LPIrate) in paraquat (Warringer et al., 2003).
An average of two replicates is given.
Author(s)
N. LeMeur
Source
Osterberg et al (2006), supplementary information:
http://www.pnas.org/content/vol0/issue2006/images/data/0604078103/DC1/04078Table1.xls
or ftp://genome-ftp.stanford.edu/pub/yeast/systematic_results/phenotypes
References
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
Examples
data(OsterbergRaw)
str(OsterbergRaw)
[Package
PCpheno version 1.4.1
Index]