hpvP35: Time-course P53 pathway data

In ragt2ridges: Ridge Estimation of Vector Auto-Regressive (VAR) Processes

Description

Time-course omics data of the P53-signalling pathway during HPV-induced transformation. Four cell lines transfected with the human papilloma virus (HPV) are cultured in petri dishes. At eight time points the cells from each cell line are molecularly interrogated genomically and transcriptomically (both mRNA and microRNA expression). From each molecular levels data DNA segments/mRNAs/microRNAs mapping to the P53-signalling pathway (as defined by KEGG, Ogata et al., 1999) are included. The included microRNAs are predicted to target the mRNAs of the pathway. Finally, two adjacency matrices are included. One describes how the DNA copy number features link to that of the mRNA expression data. The map is based on the feature's genomic location, while the other specifies which microRNAs (columns) target which mRNA (rows) according target predicton data bases. Confer Wilting et al. (2017) for preprocessing details.

Usage

data(hpvP53)

Value

hpvP53rna	An object of class ExpressionSet with the time-course mRNA expression data of 32 (=4 \mbox{ cell lines } \times 8 \mbox{ time points}) observations.
hpvP53mir	An object of class ExpressionSet with the time-course microRNA expression data of 32 (=4 \mbox{ cell lines } \times 8 \mbox{ time points}) observations.
hpvP53cn	An object of class cghRaw with the time-course DNA copy number data of 32 (=4 \mbox{ cell lines } \times 8 \mbox{ time points}) observations.
mir2rna	An object of class matrix. Adjancency matrix indicating which microRNAs (features in hpvP53mir) target which mRNAs (features in hpvP53rna). Rows = mRNAs; columns = microRNAs.
cn2rna	An object of class matrix. Adjancency matrix indicating which DNA copy number features (in hpvP53cn) map to which mRNAs (in hpvP53rna).

Source

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., Kanehisa, M. (1999), “KEGG: Kyoto Encyclopedia of Genes and Genomes”. Nucleic Acids Research, 27(1), 29-34.

Wilting, S.M., Miok, V., Jaspers, A., Boon, D., Hanne Sorgard, H., Lando, M., Snoek, B.C., Van Wieringen, W.N., Meijer, C.J.L.M., Lyng, H., Snijders, P.J.F., Steenbergen, R.D.M. (2016), “Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence”, Oncotarget, Vol. 7, No. 28, 43805-43819, DOI:10.18632/oncotarget.9698 .

Examples

data(hpvP53)

ragt2ridges documentation built on Jan. 28, 2020, 5:08 p.m.