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 1.6.0 Index]