omics {TensorTest2D}

Lung-cancer cell lines data in cancer cell line encyclopedia (CCLE) dataset

Description

The omics data is a subset of the dataset provided by cancer cell line encyclopedia (CCLE) project (Barretina et al., 2012; https://sites.broadinstitute.org/ccle/).

Usage

data(omics)

Format

A list contains two objects:

omics

a 3-dimensional array with size (3, 10, 68)

Y

a 68-length vector representing the response variable

Details

This data consists of one response variable and ten genes evaluated under three different platforms.

The response variable measures the log-transformed activity area of taking Vandertanib, a drug targeting on EGFR gene for lung cancer.

The three platforms are DNA copy number variation (CNV), methylation and mRNA expression.

Among the 10 genes, 7 of them (EGFR, EREG, HRAS, KRAS, PTPN11, STAT3, and TGFA) are involved in the protein-protein interaction network of EGFR (https://string-db.org) and the rest (ACTB, GAPDH, and PPIA) are arbitrarily chosen housekeeping genes and play the role of negative control.

Detailed pre-processing procedure is available in Chang et al. (2021).

Source

https://string-db.org

References

Barretina, J., Caponigro, G., Stransky, N. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012). (Link)

Sheng-Mao Chang, Meng Yang, Wenbin Lu, Yu-Jyun Huang, Yueyang Huang, Hung Hung, Jeffrey C Miecznikowski, Tzu-Pin Lu, Jung-Ying Tzeng, Gene-set integrative analysis of multi-omics data using tensor-based association test, Bioinformatics, 2021;, btab125, (Link))

Examples

data(omics)
names(omics)
dim(omics$omics)
# 3 10 68