Transcription factor enrichment analysis (TFEA)

TFEA is a computational method that identifies overrepresented transcription factors within a set of genes, revealing potential regulators of a biological process or pathway.

Transcription factors are proteins that can bind DNA sequences in promoter or enhancer regions to regulate the expression of genes.

Transcription factor enrichment analysis (TFEA) works to address both the position of the binding motif relative to the transcription start site and the resulting magnitude of changes in transcription activity. This allows for identification of transcription factor dynamics across a variety of data types and gene expression perturbations such as treatment with a drug. The transcription factors identified with TFEA are enriched at known binding sites within the regions of interest.

Pluto's TFEA analysis uses ChiP-X Enrichment Analysis Version 3 (ChEA3) which searches against a collection of gene sets generated from a variety of orthogonal omics experiments for improved transcription factor ranking compared to previous ChEA versions.

Transcription Factor Enrichment Analysis is available for CHiP-seq, Cut & Run and ATAC-seq experiments for all organisms and scRNA-seq for mouse and human on the Pluto platform.

Running TFEA in Pluto

In order to run TFEA, you first need to create a differential expression analysis. Once at least one differential expression analysis has been created, the Transcription factor Enrichment analysis type will become enabled in the analysis sidebar in Pluto for that experiment.

Add a new analysis, select Transcription factor Enrichment, select the TF-target gene set library you'd like to analyze with TFEA. Finally, select the comparison you'd like to use (the differential analysis you have created will appear in this list(, then click run analysis. 



As with all Pluto plots, you can customize the appearance of the score barplot using the "Plot" menu in the sidebar.

Ready to try it out on your data?


  1. Rubin, J.D., Stanley, J.T., Sigauke, R.F. et al. Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment. Commun Biol 4, 661 (2021).
  2. Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz M, Utti V, Jagodnik K, Kropiwnicki E, Wang Z, Ma'ayan A (2019) ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Research.
    doi: 10.1093/nar/gkz446