epigenomics-based Transcriptional Regulator explorer (TRex)

UMAP Projection of Pan-cancer ATAC-seq Datasets

Select rows below and click “Add to Group”.


Summary
Group
TRs > threshold
Total TRs

Top TRs (by MRRF)

Aggregation Table
Download CSV
MRRF Comparison
Venn Diagram of High Confidence TRs
MRRF Heatmap

Browse All Datasets

Run Instructions & Accession
How to Run TRex Analysis:
  1. Step 1: Upload your BED file or select an example dataset from the sidebar.
  2. Step 2: Set the genome build and analysis parameters.
  3. Step 3: Click Run TRex Analysis to start the analysis.
  4. Once the analysis is complete, the results will appear below.

Tip: Example datasets are available for both human (hg38) and mouse (mm10).

Accession Code

Similarity Network
Top Similar Datasets
Download CSV

Results Table
Download CSV

About This Application

This portal provides a user-friendly interface for the TRex analysis package. It is designed to facilitate research by allowing users to upload their data, configure parameters, and view results interactively without needing to write code.

How to Cite

If you use this application in your research, please cite the following publication:

TRex Reveals Oncogenic Transcriptional Regulatory Programs Across Human Cancers

Links & Resources

For more information, please visit the following links:

Data Acknowledgements

We gratefully acknowledge the use of publicly available datasets in this study. The pan-cancer ATAC-seq datasets were sourced from the ChIP-Atlas database, and the ChIP-seq reference datasets used for transcriptional regulator inference were obtained from the Gene Transcription Regulation Database (GTRD) .

  • Zou Z, Ohta T, Oki S. ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data. Nucleic Acids Res. 2024 Jul 5;52(W1):W45–W53. doi: 10.1093/nar/gkae358. PMID: 38749504; PMCID: PMC11223792.
  • Kolmykov S, Yevshin I, Kulyashov M, Sharipov R, Kondrakhin Y, Makeev VJ, Kulakovskiy IV, Kel A, Kolpakov F. GTRD: an integrated view of transcription regulation. Nucleic Acids Res. 2021 Jan 8;49(D1):D104–D111. doi: 10.1093/nar/gkaa1057. PMID: 33231677; PMCID: PMC7778956.

Contact Information

Developer: Zeyu Lu

Email: zeyu.lu@uta.edu

Institution: The University of Texas at Arlington, Division of Data Science & Department of Mathematics

© 2025 Xinlei Wang's lab. All Rights Reserved.

For questions, please contact Zeyu Lu .