PlanTEnrichment

PlanTEnrichment performs enrichment analysis of transposable elements (TEs) associated with specified genes or genomic regions in plant genomes, identifying enriched TE subfamilies, superfamilies, and classes.

Key Features:

• Genome Database: Includes information from 11 diverse plant genomes for cross-species TE analyses.
• Input Flexibility: Accepts lists of genes or genomic regions, including loci associated with stress responses or other biological conditions.
• TE identification and classification: Identifies TEs proximal to input regions and categorizes them by subfamily, superfamily, and class.
• Enrichment Analysis: Calculates enrichment scores and provides statistical significance measures to prioritize enriched TEs.
• Visualization Tools: Reports individual repeat instances and their genomic locations relative to input regions or genes and provides a bar graph of the top ten most significant TE subfamilies.

Scientific Applications:

• Genomic complexity and expansion: Supports studies of genomic complexity and expansion driven by transposable elements in plant genomes.
• Stress-associated TE analysis: Enables identification and analysis of stress-associated TEs near genes of interest.
• Gene expression regulation: Facilitates investigations into how TEs influence gene expression regulation.
• Evolutionary and adaptive responses: Assists in pinpointing TE subfamilies associated with particular genes or conditions to study their roles in plant genome evolution and adaptive responses.

Methodology:

Users select a target genome from the database and provide a list of genes or genomic regions; the tool identifies nearby TEs, categorizes them by subfamily, superfamily, and class, and calculates enrichment values.