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 1.52.0 Index]