DudleyPheno {PCpheno}R Documentation

List of fitness defect score generated from Dudley et al 2005

Description

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.

Usage

data(DudleyGenelist)
data(DudleyPhenoFull)
data(DudleyPhenoM)
data(DudleySign)

Format

DudleyGenelist is a character vector of length 814 genes. 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). 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.

Yname
Yeast systematic gene name
benomyl
15ug/ml benomyl,microtubule function
CaCl2
0.7M calcium chloride, divalent cation
CAD
55uM Cadmium, heavy metal
Caff
2mg/ml Caffeine
cyclohex
0.18ug/ml cycloheximide, protein synthesis
DTT
unknown
EtOH
YPD + 6% Ethanol
FeLim
iron limited, nutrient limited condition
HU
11.4mg/ml Hydroxyurea, DNA replication and repair
HygroB
50ug/ml hygromycin B, aminoglycosides
lowPO4
Low phosphate, nutrient limited condition
MPA
20ug/ml mycophenolic acid, transcriptional elongation
NaCl
1.2M sodium chloride, general stress condition
Paraq
1mM paraquat, oxidative stress
pH3
Low pH, general stress condition
rap
0.1ug/ml rapamycin, protein synthesis
Sorb
1.2M sorbitol, general stress condition
UV
100J/m2 ultra-violet, DNA replication and repair
YPGal
2% galactose, carbon source
YPGly
3% glycerol, carbon source
YPLac
2% lactate, carbon source
YPRaff
2% raffinose, carbon source

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 CoHyperGParams-class for more details) and the complexStatus function.

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 CoHyperGParams-class for more details) and the complexStatus function.

Author(s)

N. LeMeur

Source

Dudley et al (2005), supplementary information: http://arep.med.harvard.edu/pheno/default.htm

References

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. Molecular Systems Biology doi:10.1038/msb4100004

Examples

data(DudleyPhenoFull)
data(DudleyPhenoM)

[Package PCpheno version 1.2.1 Index]