Osterberg: Data from Osterberg at al. 2006

In PCpheno: Phenotypes and cellular organizational units

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)

PCpheno documentation built on Nov. 8, 2020, 5:10 p.m.