GREAM

GREAM identifies and prioritizes genomic repeat elements across 17 mammalian species by detecting and short-listing repeats that are statistically over- or under-represented in specified chromosomal regions such as gene neighborhoods.

Key Features:

• Short-listing of repeat elements: Short-lists potentially important repeat elements based on over- or under-representation within specified chromosomal locations such as gene neighborhoods.
• Categorized list generation: Generates categorized lists of transposons, retro-transposons, and other repetitive elements that are statistically over- or under-represented around genes.
• Positional and frequency analysis: Reports the genomic positions and frequencies of identified repeat elements within specified regions.
• Enrichment analysis: Performs statistical enrichment analysis of repeat sequences within chromosomal regions of interest.
• Comparative distribution analysis: Analyzes the distribution of repeats around orthologous genes across different species for comparative studies.
• Repeat classes analyzed: Detects and analyzes repeat families including LINEs, SINEs, LTRs, and other transposable elements.
• Multi-species scope: Operates across 17 mammalian species to enable cross-species comparisons.

Scientific Applications:

• Identification of functional repeats: Identified MER20 as a repeat element containing functional motifs.
• Chromosomal-region analyses: Short-listed repetitive elements in the AZFa region of the human Y chromosome.
• Disease-associated gene contexts: Short-listed repeats around genes associated with rat liver injury.
• Conserved regulatory associations: Identified five over-represented repeats near transcription factor coding genes in humans and mice with conserved expression patterns.
• Prioritization for follow-up studies: Prioritizes repeats for further experimental validation or detailed in silico analyses based on representation and location.

Methodology:

Statistical assessment of repeat over- and under-representation, generation of categorized lists, reporting of positional and frequency information, enrichment analysis, and comparative distribution analysis across orthologous genes.