bgmm (version 1.8.5)

Ste12: Ste12 knockout data under pheromone treatment versus wild type; Examples of Ste12 targets; Binding p-values of Ste12 to those targets.

Description

Ste12 knockout expression data (Roberts et al., 2002) and knowledge from a Ste12 binding experiment (Harbison et al., 2004) used for identifying Ste12 target genes under pheromone treatment.

Usage

data(Ste12)

Format

Ste12Data vector: 601 Ste12Beliefs matrix of example certainty: 42 x 2 Ste12Binding vector: 42

Details

Ste12Data Log2 expression ratios of Ste12 knockout versus wild type, both under 50nM alpha-factor treatment for 30min. This data is for 601 genes that had more than 1.5 fold change in expression after pheromone treatment versus wild type. Ste12Beliefs: Gives the certainty (belief/plausibility) for each out of 42 example Ste12 targets to belong to their cluster. Ste12Beliefs: Gives the certainty (belief/plausibility) for each out of 42 example Ste12 targets to belong to their cluster. The 42 examples were chosen to meet two criteria: (1) Had a binding p-value <0.0001 (see Ste12Binding), and (2) Had a 2-fold change in response to pheromone treatment (versus wild-type) Ste12Binding: Gives the binding p-value for each example Ste12 target (see Ste12Belief).

References

Roberts, C. J., Nelson, B., Marton, M. J., Stoughton, R., Meyer, M. R., Bennett, H. A., He, Y. D., Dai, H., Walker, W. L., Hughes, T. R., Tyers, M., Boone, C., and Friend, S. H. (2000). Signaling and Circuitry of Multiple MAPK Pathways Revealed by a Matrix of Global Gene Expression Profiles. Science, 287(5454), 873--880.

Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., Hannett, N. M., Tagne, J.-B., Reynolds, D. B., Yoo, J., Jennings, E. G., Zeitlinger, J., Pokholok, D. K., Kellis, M., Rolfe, P. A., Takusagawa, K. T., Lander, E. S., Gifford, D. K., Fraenkel, E., and Young, R. A. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431(7004), 99--104.

See Also

miRNA,CellCycle

Examples

# NOT RUN {
    data("Ste12")
    print(Ste12Data)
    print(Ste12Beliefs)
    print(Ste12Binding)
# }