Dudley: List of fitness defect score generated from Dudley et al 2005

In PCpheno: Phenotypes and cellular organizational units

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)

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