NiederbergerMediator2012: Expression measurements upon perturbation of Mediator...

In nem: (Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

Description

This dataset combines expression data from 4 gene perturbation studies in S. cerevisae, including the perturbations of the 9 Mediator subunits Med2, Med7 (N-terminus), Med7 (C-terminus), Med10, Med15, Med19, Med20, Med21 and Med31. Med10 and Med21 have been combined due to indistinguishable results.

Usage

data(NiederbergerMediator2012)

Format

NiederbergerMediatorLods: data matrix(log-odds ratios): 2578 x 8 NiederbergerMediatorLogFC: data matrix(log2 fold-changes): 2578 x 8 NiederbergerMediatorPVals: data matrix(p-values): 2578 x 8

Details

The data has been preprocessed using the R/Bioconductor package limma. The results have been filtered as follows: The original data contains a double-knockout Med7N/Med31, which can't be assessed by EMiNEM and has thus been removed. Analysis of the data revealed genes showing batch-specific effects, they have been excluded from further analysis. Finally, genes that do not react to any perturbation have been removed since they do not contain additional information. For a more detailed description of the individual studies and datasets as well as further information on data processing and results, please refer to Niederberger et al, 2012. The raw data is available on Array Express (accession number [provided upon publication]).

NiederbergerMediatorLods: the log-odds ratios NiederbergerMediatorLogFC: the log2 fold-changes NiederbergerMediatorPVals: the corresponding p-values

References

Niederberger T., Etzold S., Lidschreiber M., Maier K.C., Martin D.E., Fr\"o hlich H., Cramer P., Tresch A., MC EMiNEM Maps the Interaction Landscape of the Mediator. PLoS Computational Biology, 8(6): e1002568, 2012-

Examples

    data(NiederbergerMediator2012)
    dim(NiederbergerMediatorLods)
    dim(NiederbergerMediatorLogFC)
    dim(NiederbergerMediatorPVals)

nem documentation built on Oct. 31, 2019, 2:12 a.m.