GiaeverPheno {PCpheno} | R Documentation |
Giaever et al (2002) 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 six different experimental conditions.
data(GiaeverPheno) data(GiaeverGene) data(GiaeverExpCdt)
GiaeverPheno
is a list with 31 elements. The name of each
element is a experimental condition (see details). The value of each
element are the fitness defect scores for the genes sensitive to the
experimental condition, as defined by Giaever et al (2002).
GiaeverGene
Vector of the systematic gene names of the 5898 tested
genes. Note that some updates have been made for the list to be
consistent with Saccharomyces Genome Database.
GiaeverExpCdt
is a 3 columns dataframe with fileID from
which the data were extracted, the generation time (growth time) and
the condition (media).
Note: in their study they confound the 15 and 20 generations.
Giaeverresult
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
Giaever et al (2002), supplementary information: http://genomics.lbl.gov/YeastFitnessData/websitefiles/cel_index.html Saccharomyces Genome Database (last update 03/17/06): http://www.yeastgenome.org/
Giaever G et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418(6896):387-91. PMID: 12140549
data(GiaeverPheno) data(GiaeverExpCdt) data(GiaeverGene)