foroutan2017_se: TGFb stimulated cell lines from Foroutan et al. (2017)

In DavisLaboratory/emtdata: An ExperimentHub Package for data sets with an Epithelial to Mesenchymal Transition (EMT)

Description

Foroutan et al. collected data from multiple different studies where various cell lines (from various tissues of origin) were stimulated with transforming growth factor beta (TGFb) to induce an epithelial to mesenchymal transition (EMT). Since the data were from different studies (and platforms), the surrogate variable analysis (SVA) and ComBat approaches were applied to correct for batch effects.

Format

A SummarizedExperiment object, containing gene expression data of human cell lines treated with TGFb. The SummarizedExperiment::colData() function can be used to access the sample annotations.

Details

Data from this publication were downloaded from figshare and processed into a SummarizedExperiment object. Sample annotations were retrieved from the original publication.

References

Foroutan, M., Cursons, J., Hediyeh-Zadeh, S., Thompson, E. W., & Davis, M. J. (2017). A transcriptional program for detecting TGFb-induced EMT in Cancer. Molecular Cancer Research, 15(5), 619-631.

Examples

library(ExperimentHub)
eh <- ExperimentHub()
emt_datasets <- query(eh, "emtdata")

DavisLaboratory/emtdata documentation built on Dec. 17, 2021, 4:09 p.m.