{
  "abstract": "Background\n\nApproximately 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\n\nTo 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\n\nWith 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.",
  "abstract_shown": true,
  "affiliations": [
    "Quantitative Life Sciences, McGill University, Montréal, QC, Canada. jeffrey.hyacinthe@mail.mcgill.ca.",
    "Canadian Center for Computational Genomics, McGill University, Montréal, QC, Canada.",
    "Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada.",
    "Department of Human Genetics, McGill University, Montréal, QC, Canada. guil.bourque@mcgill.ca.",
    "Canadian Center for Computational Genomics, McGill University, Montréal, QC, Canada. guil.bourque@mcgill.ca.",
    "Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada. guil.bourque@mcgill.ca."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Jeffrey Hyacinthe",
      "orcid": "0009-0005-0767-4731"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "David R Lougheed",
      "orcid": "0000-0003-0962-543X"
    },
    {
      "affs": [
        3,
        4,
        5
      ],
      "name": "Guillaume Bourque",
      "orcid": "0000-0002-3933-9656"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8dpdz3x4b8c3b.bib",
  "cited_by": 0,
  "doi": "10.1186/s12864-026-13215-7",
  "fulltext_url": "https://europepmc.org/articles/PMC13726177",
  "id": "8dpdz3x4b8c3b",
  "issns": [
    "1471-2164"
  ],
  "landing_url": "https://europepmc.org/article/MED/42972241",
  "language": "eng",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Software"
    ],
    [
      "openalex",
      "1110|Chromosomal and Genetic Variations"
    ]
  ],
  "openalex": "W7172493855",
  "pdf_url": "https://europepmc.org/articles/PMC13726177?pdf=render",
  "pmcid": "PMC13726177",
  "pmid": "42972241",
  "published": "2026-08-05",
  "publisher": "BMC",
  "ris": "https://research.draconitic.com/paper/8dpdz3x4b8c3b.ris",
  "sources": [
    {
      "first_seen": "2026-11-04T15:20:49Z",
      "native_id": "MED:42972241",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42972241"
    },
    {
      "first_seen": "2026-11-05T12:22:35Z",
      "native_id": "PMC13726177",
      "source": "pmc",
      "url": "https://doi.org/10.1186/s12864-026-13215-7"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1110|Chromosomal and Genetic Variations",
      "subfield": "plant-biology"
    }
  ],
  "title": "TEExplorer: a web portal to investigate TE-epigenome associations across human cell types.",
  "title_text": "TEExplorer: a web portal to investigate TE-epigenome associations across human cell types.",
  "type": "peer-reviewed",
  "updated_at": "2026-11-06T12:22:12Z",
  "url": "https://research.draconitic.com/paper/8dpdz3x4b8c3b",
  "venue": "BMC genomics",
  "versions": []
}