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bioRxiv · 10.1101/2020.01.25.919738

Transcription factor enrichment analysis (TFEA): Quantifying the activity of hundreds of transcription factors from a single experiment

Rubin, J. D.·Stanley, J. T.·Sigauke, R. F.·Levandowski, C. B.·Maas, Z. L.·Westfall, J.·Taatjes, D. J.·Dowell, R. D.
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Abstract

1Detecting differential activation of transcription factors (TFs) in response to perturbation provides insight into cellular processes. Transcription Factor Enrichment Analysis (TFEA) is a robust and reliable computational method that detects differential activity of hundreds of TFs given any set of perturbation data. TFEA draws inspiration from GSEA and detects positional motif enrichment within a list of ranked regions of interest (ROIs). As ROIs are typically inferred from the data, we also introduce muMerge, a statistically principled method of generating a consensus list of ROIs from multiple replicates and conditions. TFEA is broadly applicable to data that informs on transcriptional regulation including nascent (eg. PRO-Seq), CAGE, ChIP-Seq, and accessibility (e.g. ATAC-Seq). TFEA not only identifies the key regulators responding to a perturbation, but also temporally unravels regulatory networks with time series data. Consequently, TFEA serves as a hypothesis-generating tool that provides an easy, rigorous, and cost-effective means to broadly assess TF activity yielding new biological insights.

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Rubin, J. D., Stanley, J. T., Sigauke, R. F., Levandowski, C. B., Maas, Z. L., Westfall, J., Taatjes, D. J., Dowell, R. D.. 2020-01-25. Transcription factor enrichment analysis (TFEA): Quantifying the activity of hundreds of transcription factors from a single experiment. https://doi.org/10.1101/2020.01.25.919738

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