Satellog

Satellog catalogs and prioritizes pure 1–16 repeat unit satellite repeats in the human genome to support disease association studies by integrating polymorphism data, genomic context, and expression profiles.

Key Features:

• Comprehensive cataloging: Contains over 5,546 pure 1–16 repeat unit satellite repeats identified within the human genome.
• Polymorphism analysis: Assesses evidence of polymorphism for each repeat using UniGene clusters and reports that polymorphic repeats are over-represented in 3'-UTR sequences compared to 5'-UTR and coding sequences.
• Repeat polymorphism insights: Notes that within coding sequences only trinucleotide repeats exhibit polymorphism, while UTR sequences accommodate a broader range of repeat period polymorphisms.
• Prioritization criteria: Prioritizes repeats based on repeat unit, class, period, length, repeat length percentile rank, genomic coordinates, polymorphism profiles within UniGene, presence or proximity to gene regions (coding sequences, UTRs), and metadata of associated genes.
• Expression profile integration: Integrates expression profile data from the GeneNote database to provide expression context in normal human tissues.
• Disease association evaluation: Evaluates properties of unstable repeats associated with 31 diseases to identify common characteristics relevant to disease etiology.

Scientific Applications:

• Repeat expansion disorder research: Supports studies of genetic disorders characterized by repeat expansions, including Huntington's disease and schizophrenia, by enabling prioritization of candidate satellite repeats.

Methodology:

Cataloged satellite repeats from the human genome; analyzed polymorphism within UniGene clusters; calculated repeat length percentile ranks and genomic coordinates relative to EnsEMBL genes; integrated GeneNote expression profiles; and prioritized repeats based on repeat unit, class, period, length, percentile rank, polymorphism profiles, and genomic context.