MM {cglasso}

The Rule of miRNA in Multiple Myeloma

Description

MicroRNAs (miRNAs) are endogenous small non-coding RNAs, approximately 22 nucleotides in length, that play a regulatory role in gene expression by mediating mRNA cleavage or translation expression. Several studies have shown that a deregulation of the miRNAs can cause a disruption in the gene regulation mechanisms of the cell and that this might even lead to cancerous phenotypes.

Gutierrez and others (2010) investigated the expression level of a set of 141 miRNAs, measured by RT-qPCR technology on a sample of 64 patients with multiple myeloma (MM). Patients were selected to represent the most relevant recurrent genetic abnormalities in MM. RT-qPCR data are typically right-censored and, in this study, the upper limit of detection was fixed to 40 cycles.

Formally, MM is a list with containing a subset of the date studied in Gutierrez and others (2010). Its components are:

• Y: the response matrix containing the cycle-threshold of the measured 49 miRNAs;

• X: the predictor matrix containing the expression levels of 15 endogenous internal reference genes, called housekeeping, and a factor encoding the cytogenetic abnormalities.

Usage

data("MM")

References

Augugliaro L., Sottile G., Wit E.C., and Vinciotti V. (2023) <doi:10.18637/jss.v105.i01>. cglasso: An R Package for Conditional Graphical Lasso Inference with Censored and Missing Values. Journal of Statistical Software 105(1), 1–58.

Augugliaro, L., Sottile, G., and Vinciotti, V. (2020) <doi:10.1007/s11222-020-09945-7>. The conditional censored graphical lasso estimator. Statistics and Computing 30, 1273–1289.

Augugliaro, L., Abbruzzo, A., and Vinciotti, V. (2020) <doi:10.1093/biostatistics/kxy043>. \ell_1-Penalized censored Gaussian graphical model. Biostatistics 21, e1–e16.

Gutierrez, N. Sarasquete, M., Misiewicz-Krzeminska, I., Delgado, M. De Las Rivas, J., Ticona, F.V., Ferminan, E., Martin-Jimenez, P., Chillon, C., Risueno, A., Hernandez, J.M., Garcia-Sanz, R., Gonzalez, M. and San Miguel, J.F. (2010) <doi:10.1038/leu.2009.274>. Deregulation of microRNA expression in the different genetic subtypes of multiple myeloma and correlation with gene expression profiling. Leukemia 24(3), 629–637.

See Also

cglasso, to_graph, and the method functions summary, coef, plot, AIC.cglasso and BIC.cglasso.

Examples

data("MM")
Z <- datacggm(Y = MM$Y, X = MM$X, up = 40)
print(Z, width = 80L)