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Peer-reviewedCC BY-NC-NDBMC genomics

TEExplorer: a web portal to investigate TE-epigenome associations across human cell types.

  • Jeffrey Hyacinthe1
  • David R Lougheed2,3
  • Guillaume Bourque4,5,6
6 affiliations
  1. 1Quantitative Life Sciences, McGill University, Montréal, QC, Canada. [email protected].
  2. 2Canadian Center for Computational Genomics, McGill University, Montréal, QC, Canada.
  3. 3Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada.
  4. 4Department of Human Genetics, McGill University, Montréal, QC, Canada. [email protected].
  5. 5Canadian Center for Computational Genomics, McGill University, Montréal, QC, Canada. [email protected].
  6. 6Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada. [email protected].
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Abstract

Background

Approximately half of the human genome is derived from transposable elements (TEs) and several studies support the involvement of TEs in genome regulation in development, immunity and disease. We previously leveraged 4614 ChIP-seq samples from the International Human Epigenome Consortium (IHEC) EpiATLAS dataset and did a comprehensive analysis of the relationship between TEs and 6 histone marks across 57 human cell types. However, with over 6 million measurements of TE / histone mark / cell type enrichment, it was challenging to navigate the results and it was not possible to integrate them with user data.Results

To address this, we developed a web tool, TEExplorer, which makes available TE overlaps and enrichments in an accessible and intuitive manner. The tool presents an interactive view of TE families and subfamilies, with their overlap and enrichments across histone marks and cell types. Finally, the tool allows users to upload their own ChIP-seq BED file to obtain the TE overlap and enrichment relative to random controls and compare their data with the EpiATLAS dataset.Conclusions

With TEExplorer, researchers with an interest in a particular TE family or subfamily, histone mark, or cell type, or those bringing their own ChIP-seq dataset, can dynamically explore and contrast hundreds of associations found within the large EpiATLAS dataset.

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Cite

BibTeXRIS
BibTeX
@article{hyacinthe2026teexplorer,
  title = {{TEExplorer: a web portal to investigate TE-epigenome associations across human cell types.}},
  author = {Jeffrey Hyacinthe and David R Lougheed and Guillaume Bourque},
  journal = {BMC genomics},
  year = {2026},
  month = aug,
  doi = {10.1186/s12864-026-13215-7},
  url = {https://europepmc.org/article/MED/42972241},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - TEExplorer: a web portal to investigate TE-epigenome associations across human cell types.
AU  - Jeffrey Hyacinthe
AU  - David R Lougheed
AU  - Guillaume Bourque
PY  - 2026
DA  - 2026/08/05
JO  - BMC genomics
DO  - 10.1186/s12864-026-13215-7
UR  - https://europepmc.org/article/MED/42972241
AB  - Background  Approximately half of the human genome is derived from transposable elements (TEs) and several studies support the involvement of TEs in genome regulation in development, immunity and disease. We previously leveraged 4614 ChIP-seq samples from the International Human Epigenome Consortium (IHEC) EpiATLAS dataset and did a comprehensive analysis of the relationship between TEs and 6 histone marks across 57 human cell types. However, with over 6 million measurements of TE / histone mark / cell type enrichment, it was challenging to navigate the results and it was not possible to integrate them with user data.Results  To address this, we developed a web tool, TEExplorer, which makes available TE overlaps and enrichments in an accessible and intuitive manner. The tool presents an interactive view of TE families and subfamilies, with their overlap and enrichments across histone marks and cell types. Finally, the tool allows users to upload their own ChIP-seq BED file to obtain the TE overlap and enrichment relative to random controls and compare their data with the EpiATLAS dataset.Conclusions  With TEExplorer, researchers with an interest in a particular TE family or subfamily, histone mark, or cell type, or those bringing their own ChIP-seq dataset, can dynamically explore and contrast hundreds of associations found within the large EpiATLAS dataset.
SN  - 1471-2164
ER  -