ArticleCommunications biology2021
Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- Probing transcription factor subsets in gene regulatory networks.Algorithms for molecular biology : AMB · 2026Article
- Fruitless produces diverse neuronal sex differences by editing lineage-programmed chromatin landscapes.bioRxiv : the preprint server for biology · 2026Article
- Improving calls of differentially transcribed enhancers and their upstream regulators.Bioinformatics advances · 2026Article
- Multi-omics to study chronic respiratory diseases and viral infections.European respiratory review : an official journal of the European Respiratory Society · 2026Review
- Integrative Multimodal Profiling of TAp73 and DNp73 Reveals Isoform-Specific Transcriptomic Coregulator Landscapes in Cancer Programs.Biomolecules · 2025Article
- Dmrt2 regulates sex-biased neuronal development in the cingulate cortex.Cellular and molecular life sciences : CMLS · 2025Article
- Improving confidence of differential transcription calls in enhancers.bioRxiv : the preprint server for biology · 2025Article
- PRMT5 activity sustains histone production to maintain genome integrity.bioRxiv : the preprint server for biology · 2025Article
- Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.BMC genomics · 2025Article
- LIET model: capturing the kinetics of RNA polymerase from loading to termination.Nucleic acids research · 2025Article
- TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks.Genome biology · 2025Article
- TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network.Science advances · 2025Article
- Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome.eLife · 2025Article
- Roles of Post-Translational Modifications of Transcription Factors Involved in Breast Cancer Hypoxia.Molecules (Basel, Switzerland) · 2025Review
- RNAseq of peripheral blood mononucleated cells exposed to platelet-rich fibrin and enamel matrix derivatives.Scientific reports · 2025Article
- Evaluation of large language models for discovery of gene set function.Nature methods · 2025Article
- Benchmarking tools for transcription factor prioritization.Computational and structural biotechnology journal · 2024Article
- Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome.bioRxiv : the preprint server for biology · 2024Article
- Iron-(Fe3+)-Dependent Reactivation of Telomerase Drives Colorectal Cancers.Cancer discovery · 2024Article
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Authors and funding
8 authors.
Funding
Abstract
Detecting changes in the activity of a transcription factor (TF) in response to a perturbation provides insights into the underlying cellular process. Transcription Factor Enrichment Analysis (TFEA) is a robust and reliable computational method that detects positional motif enrichment associated with changes in transcription observed in response to a perturbation. TFEA detects positional motif enrichment within a list of ranked regions of interest (ROIs), typically sites of RNA polymerase initiation inferred from regulatory data such as nascent transcription. Therefore, 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 transcription (eg. PRO-Seq), CAGE, histone ChIP-Seq, and accessibility data (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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.