Ivanova2006RNAiTimeSeries: Perturbation Time Series

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

Description

The dataset consists of time series microarray measurements (only 1 replicate, 6 time points) for RNAi knock-downs of each of the six genes Nanog, Oct4, Sox2, Esrrb, Tbx3, and Tcl1 in mouse embryonic stem cells.

Usage

data(Ivanova2006RNAiTimeSeries)

Format

dat: 8 x 122 x 6 array of discretized time series data for E-genes showing a abs(logFC) > 1 in at least one time point (see Anchang et al., 2009).

Details

Mouse embryonic stem cells (ESCs) were grown in the presence of leukemia inhibitory factor (LIF), thus retaining their undifferentiated self-renewing state (positive controls). Differentiation associated changes in gene expression were measured by replacing LIF with retinoic acid (RA), thus inducing differentiation of stem cells (negative controls). RNAi silencing of the 6 afore mentioned genes was done in (LIF+, RA-) cell culturs to investigate their potential for induced cell differentiation. Microarray expression measurements at 6 - 7 time points in one-day intervals were taken for the two controls (positive and negative) and the six RNAi assays. The dataset by Ivanova et al. (2006) was measured once on Affymetrix MOE430A and once on MOE430B chips. The authors normalized both datasets via the MAS 5.0 software (Hubbell et al., 2002). Here, only the Affymetrix MOE430A chip series is included.

References

Ivanova, N., Dobrin, R., Lu, R., Kotenko, I., Levorse, J., DeCoste, C., Schafer, X., Lun, Y., and Lemischka, I. R. (2006). Dissecting self-renewal in stem cells with RNA interference. Nature, 442(7102):533-538.\

Anchang, B., Sadeh, M. J., Jacob, J., Tresch, A., Vlad, M. O., Oefner, P. J., and Spang, R. (2009). Modeling the temporal interplay of molecular signaling and gene expression by using dynamic nested effects models. Proceedings of the National Academy of Sciences of the United States of America, 106(16):6447-52.

See Also

Ivanova2006RNAiTimeSeries

Examples

    data("Ivanova2006RNAiTimeSeries")
    dim(dat)          

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