TEENA: an integrated web server for Transposable Element ENrichment Analysis in given genomic regions

Transposable elements (TEs) are abundant in the genomes of various animals and plants. While long been regarded as “junk DNA”, accumulated data suggest the crucial roles of TEs, frequently by creating regulatory elements (particularly enhancers and promoters) bound by distinct transcription factors (TFs). TE-derived regulatory elements have gained unprecedented attentions in recent years, and one key step toward their understanding is to identify the TE families enriched in interested genomic regions (e.g. a set of enhancers or TF binding sites), which can then be subjected to in-depth analysis and validation. Nevertheless, such analysis remains challenging for researchers either unfamiliar with TEs or lack sophisticated bioinformatic skills, which severely hinders the study of TE function.

Here, we presented TEENA (Transposable Element ENrichment Analyzer), which is an integrated web server to streamline TE enrichment analysis in a variety of model and non-model animal species. It implements an optimized pipeline, integrates the genome/gene/TE annotations, and provides multiple parameters to enable substantial flexibility. Taking genomic interval data as the only required file, it can automatically retrieve the annotations for corresponding species and finish a routine analysis in a couple minutes. Apart from basic enrichment statistics, it also provides multiple tables and figures to facilitate result interpretation and candidate TE/gene selection. We hope that it will facilitate future studies on the regulation and function of TEs in different model and non-model animal species.

TEENA is freely accessible to everyone, including commercial users.