PlanTEnrichment
Transposable elements (TEs) are DNA fragments that can move and integrate themselves into novel sites within host genome. Previous studies indicate that these mobile genetic elements are associated with gene regulation, and have a potential to influence the expression of nearby genes by functioning as cis-regulatory sequences (for review see Elbarbary et al. 2016 - Hirsch and Springer 2017). Bioinformatics tools facilitating analysis of the associations between TEs and nearby genes in plants are still lacking despite their significance as novel regulatory elements. We therefore reanalyzed the comprehensive annotation data of gene models and TEs of 11 plant species available in Ensembl Plants database, and identified TEs located within 1, 2.5 and 5 kb upstream regions of plant genes, respectively. Afterwards, we developed an up-to-date, unique tool called PlanTEnrichment, which permits enrichment analysis of TEs located within the upstream regions of a given gene list. By an approach similar to that used in GO term enrichment analysis, PlanTEnrichment takes, for example, a group of genes sharing a common feature (e.g. differentially expressed genes between normal and stress conditions) and returns a list of candidate TEs that have a potential to serve as novel regulatory sequences for nearby genes, along with their calculated enrichment scores and statistical significances.