Cell types TE enrichments
TE SubFamilies Contribution
Data table
Transposable Elements Mean Overlap
Transposable Elements enrichment overview
Transposable Elements Mean enrichment Per Mark
Import File
File List
Overlap Overview
TE overlap of uploaded sample(s) peaks compared to EpiATLAS and random data
Metric
Enrichments (Observed - Expected, fold change) are calculated relative to the Random overlap obseved within EpiATLAS' corresponding dataset (selected cell type and histone)
Highlight
TE Enrichment Overview Heatmap
TE Family Enrichment
TE subfamilies Enrichment
Up to top 40 most enriched TE subfamilies displayed
Data table
About
TEExplorer
Version 0.987
2-2026
methods
EpiATLAS TE measurements
EpiATLAS histone peak files (hg38) had their peaks resized to 200bp and then were overlapped with TEs from repeatmaskers. For each subfamily the number of overlap was tallied for the count overlap metric. For each sample, an associated simulated random sample was generated. These samples were generated such that they matched the peak distribution of distances to TSS.
Enrichment calculations
The enrichments, observed-expected and fold change are calculated from the observed count, relative to the count obseved in the random samples. Thus, observed count - expected count and observed count / expected count respectively.
Understanding Enrichments (Include depleted)
For every sample, each TE subfamily overlap count was measured along with simulated random controls, the count was compared to the random count for each iteration. the Expected count is the mean of 1000 simulation. In addition, we deemed a TE significantly enriched if its count was higher than random 995/1000 times. By default (In TE subfamilies tab), only significant TEs are used. Inherently, the expected count are always lower and thuse obs-exp is always positive. Include depleted ignores the significance of the measurement and enables observing depleted TEs.
Uploaded samples comparisons
Uploaded samples are taken as is and overlapped to the TEs from repeatmasker (hg38). Enrichments are calculated relative to the expected counts from average counts of the random samples associated with the selected assay and Cell type (from the EpiATLAS). This is important to note as the random baseline is purely random nor generated from the uploaded sample.
In boxplot, stars are the significance of Wilcoxon test comparison **** = pval< 1e-04; *** = pval<0.001; ** = pval<0.01; * = pval<0.05
If 'All' Cell type is selected, random baselines are calculated from the average of all cell types combined.
Dataset based on IHEC's EpiATLAS data and TE measurements from Hyacinthe et al. 2024
Hyacinthe, J. & Bourque, G. Transposable elements impact the regulatory landscape through cell type specific epigenomic associations. 2024.08.07.606967 Preprint at https://doi.org/10.1101/2024.08.07.606967 (2024).
EPiAtlas Data: https://ihec-epigenomes.org/epiatlas/data/
IHEC: https://epigenomesportal.ca/ihec/
TE annotations based on repeatmasker
Tool by Jeffrey Hyacinthe
Bourque Lab 2026
Change log
0.987 (2-2026): Minor issue fixes, preprint submition
0.985 (10-2025): Minor issue fixes
0.980 (05-2025): Minor issue fixes, import demo file, legend order match
0.950 (03-2025): Minor issue fixes, Auto load default result pages, caching
0.900 (09-2024): First public release
TEExplorer
TEExplorer is a TE portal that simplifies TE consideration by providing an atlas of TE enrichment within the epigenome that can be explored through specific queries. The Atlas cover 6 histone marks, over 40 cell types from the IHEC EpiATLAS dataset. In addition the portal allows the analysis of TE overlap within user uploaded Bed files and straightforward comparison with the atlas' data.
TE Overview
Overview of TE family enrichement across cell types and histone marks. Select TE, Histone and Cell types of interest for more specific inquiry.
TE Subfamilies
Investigate the subfamilies of a specific TE family and their overlap or enrichment within a histone across cell types
Import
Upload your own hg38 bed file to and obtain the TE overlap, TE enrichment visualization and compare your data with the EpiATLAS dataset
TEExplorer
TEExplorer is a TE portal that simplifies TE consideration by providing an atlas of TE enrichment within the epigenome that can be explored through specific queries. The Atlas cover 6 histone marks, over 40 cell types from the IHEC EpiATLAS dataset. In addition the portal allows the analysis of TE overlap within user uploaded Bed files and straightforward comparison with the atlas' data.