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Table 1 Recovering epithelial to mesenchymal transition transcriptional regulators

From: xcore: an R package for inference of gene expression regulators

Top signatures

A-549

MDA-231-D

ISMARA

Lisa

xcore

ISMARA

Lisa

xcore

ReMap2020

ChIP-Atlas

ReMap2020

ChIP-Atlas

1–10

SMAD4

SMAD3, SMAD4, GATA3

SMAD3, SMAD2

SMAD3, SMAD2, SMAD4

 

SMAD4, SMAD3

SMAD3, SMAD4

SMAD3, SMAD4, SMAD2, GATA3

11–50

 

FOXA2, FOXA1

EZH2, GATA3, SMAD4

EZH2, FOXA2

SMAD4

GATA3

SMAD2

EZH2, FOXA2, FOXA1

51–100

GATA3, FOXA1

NKX2-1, TCF7L2

FOXA1, FOXA2, NKX2-1

FOXA1, GATA3

 

FOXA1, NKX2-1

EZH2, FOXA1

 
  1. Table summarizing EMT-related transcriptional regulators recovered by ISMARA, Lisa and xcore among their top-scoring signatures based on TGFβ induced EMT CAGE datasets. The list of EMT-related transcriptional regulators used to assess the recovery was constructed using Gene Ontology term regulation of epithelial to mesenchymal transition (GO:0010717) by including only regulators available in the references of all tools