EMTscoreData

EMTscoreData is an R data package that provides curated gene expression datasets for benchmarking and developing epithelial–mesenchymal transition (EMT) scoring methods. This package is prepared as the companion dataset for the upcoming EMTscore R package.

Overview

EMTscoreData includes processed expression data and metadata derived from the public dataset:

GSE147405 (Cook et al.)
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147405

This study performed a MULTI-seq pooled experiment using four human epithelial cancer cell lines:

• A549
• DU145
• MCF7
• OVCA420

Cells were treated with TGFB1, EGF, or TNF for multiple time periods to capture dynamic changes related to EMT and cellular state transitions.

Package Contents

The package provides:

• Processed gene expression matrices (e.g., log-normalized counts)
• Cell-level metadata including:
  • cell line
  • treatment
  • time point
• Objects are stored in R-friendly formats as SingleCellExperiment (.rda) objects for convenient downstream analysis.

These datasets are ready to use for:

• EMT scoring method development
• Benchmarking EMT/MET signatures

Installation

Install from GitHub:

# install.packages("devtools")
devtools::install_github("wenmm/EMTscoreData")

Data Source and Citation

The dataset included in this package is derived from:

Cook DP, et al.
Cook DP, Vanderhyden BC. Context specificity of the EMT transcriptional response. Nat Commun 2020 May 1;11(1):2142. PMID: 32358524
GEO accession: GSE147405

If you use EMTscoreData in your work, please cite both Cook DP, et al. and the EMTscore package (once it is published).