DudleyPheno {PCpheno} | R Documentation |
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.
data(DudleyGenelist) data(DudleyPhenoFull) data(DudleyPhenoM) data(DudleySign)
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.
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.
N. LeMeur
Dudley et al (2005), supplementary information: http://arep.med.harvard.edu/pheno/default.htm
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
data(DudleyPhenoFull) data(DudleyPhenoM)