tcga_brca_testdata: Breast cancer expression test data from TCGA

In Mirsynergy: Mirsynergy

Description

Test data of 2661 mRNA and 142 miRNA (i.e., 0.2 of the whole data) across 15 tumor samples from breast cancer (BRCA) patients. The data were downloaded from TCGA (The Cancer Genome Atlas). The full BRCA expression data contain expression measurements for 13306 and 710 distinct mRNAs and miRNAs across 331 samples.

Format

A list containing the follow items:

X,Z

N-by-T and M-by-T Expression matrices for N mRNA and M miRNA measured across T samples

C,H

N-by-M and N-by-N matrices for sequence-based miRNA-targets downloaded from TargetScanHuman 6.2 and gene-gene interactions from TRANSFAC and BioGrid invoving transcription factor binding sites (TFBS) and protein-protein interactions, respectively.

References

Cancer Genome Atlas Research Network (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455(7216), 1061-1068.

Friedman, R. C., Farh, K. K.-H., Burge, C. B., and Bartel, D. P. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Research, 19(1), 92-105.

Examples

load(system.file("extdata/tcga_brca_testdata.RData", package="Mirsynergy"))

Mirsynergy documentation built on April 28, 2020, 6:09 p.m.