bgmm (version 1.8.5)

CellCycle: Data for clustering of 384 cell cycle genes into five clusters corresponding to cell cycle phases

Description

Time course expression data for 384 cell cycle genes (Cho et al., 1998). Literature examples of genes that should, and of genes that should not peak at each time point are given. For each cycle phase, there is a characteristic binary profile, stating when the phase occurs.

Usage

data(CellCycle)

Format

CellCycleData list: 17x384 CellCycleBeliefs list: 17x (35x2) CellCycleCenters matrix: 5x17 CellCycleClass vector: 384

Details

CellCycleData: A list, where each entry corresponds to one time-point. A given time point entry contains a vector with expression ratios for 384 cell cycle genes measured in this time point. CellCycleBeliefs: A list, where each entry corresponds to one time-point. A given time point entry gives the certainty (belief/plausibility) for each out of 35 example genes. Out of the genes, seven are known to peak in this time point and the remaining 28 are known to peak in other cycle phases. CellCycleCenters: A matrix, where the columns are the 17 time-points and the rows to the five cell phase clusters. A given entry in the matrix is equal to 1 if the genes from the cluster should peak in the time point, and 0 otherwise. CellCycleClass:Gives the true cluster for each gene. Each cluster corresponds to a cell cycle phase.

References

Cho, R., Campbell, M., Winzeler, E., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T., Gabrielian, A., Landsman, D., Lockhart, D., and Davis, R. (1998). A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell, 2(1), 65--73.

See Also

miRNA,Ste12

Examples

# NOT RUN {
library(bgmm)
data(CellCycle)
print(CellCycleData)
print(CellCycleBeliefs)
print(CellCycleCenters)
print(CellCycleClass)
# }