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. 2024 Jul 5;52(W1):W126-W131.
doi: 10.1093/nar/gkae411.

TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms

Yuzhuo Li  1 , Renzhe Lyu  1 , Shuai Chen  1 , Yejun Wang  2 , Ming-An Sun  1   3   4   5
Affiliations

TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms

Yuzhuo Li et al. Nucleic Acids Res. .

Abstract

Transposable elements (TEs) are abundant in the genomes of various eukaryote organisms. Increasing evidence suggests that TEs can play crucial regulatory roles-usually by creating cis-elements (e.g. enhancers and promoters) bound by distinct transcription factors (TFs). TE-derived cis-elements have gained unprecedented attentions recently, and one key step toward their understanding is to identify the enriched TEs in distinct genomic intervals (e.g. a set of enhancers or TF binding sites) as candidates for further study. Nevertheless, such analysis remains challenging for researchers unfamiliar with TEs or lack strong bioinformatic skills. Here, we present TEENA (Transposable Element ENrichment Analyzer) to streamline TE enrichment analysis in various organisms. It implements an optimized pipeline, hosts the genome/gene/TE annotations of almost one hundred species, and provides multiple parameters to enable its flexibility. Taking genomic interval data as the only user-supplied file, it can automatically retrieve the corresponding annotations and finish a routine analysis in a couple minutes. Multiple case studies demonstrate that it can produce highly reliable results matching previous knowledge. TEENA can be freely accessed at: https://sun-lab.yzu.edu.cn/TEENA. Due to its easy-to-use design, we expect it to facilitate the studies of the regulatory function of TEs in various model and non-model organisms.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Performance evaluation of the TEENA method. This figure shows the comparison across TEENA, BEDtools fisher and GIGGLE for TE enrichment analysis. (A–C) Comparison of the fold enrichment. (D–F) Comparison of the P-values. The STAT1 peaks in IFNγ-stimulated human CD14+ macrophages were used for analysis. The Pearson's r and P-values are indicated.
Figure 2.
Figure 2.
Case studies by applying TEENA. This figure shows the case study results on four datasets. (A) STAT1 peaks in IFNγ-stimulated human CD14+ macrophages; (B) GATA3 peaks in human TSCs; (C) H3K27ac peaks in human TSCs; (D) CTCF peaks in pig spleen. The ten most significant LTRs/ERVs are shown. The x-axis indicates the –log10(P), and the color gradients indicate the fold enrichment.
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