ArticleBMC bioinformatics2005
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Inhibition of nonsense-mediated decay in TDP-43 deficient neurons reveals novel cryptic exons.bioRxiv : the preprint server for biology · 2025Article
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- A microsatellite repeat in PCA3 long non-coding RNA is associated with prostate cancer risk and aggressiveness.Scientific reports · 2017Article
- FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent.BMC genomics · 2013Article
- RiDs db: Repeats in diseases database.Bioinformation · 2011Article
- Database of exact tandem repeats in the Zebrafish genome.BMC genomics · 2010Article
- Exploring the relationship between polymorphic (TG/CA)n repeats in intron 1 regions and gene expression.Human genomics · 2009Article
- An online conserved SSR discovery through cross-species comparison.Advances and applications in bioinformatics and chemistry : AABC · 2009Article
- UgMicroSatdb: database for mining microsatellites from unigenes.Nucleic acids research · 2008Article
- EuMicroSatdb: a database for microsatellites in the sequenced genomes of eukaryotes.BMC genomics · 2007Article
- A novel trinucleotide repeat expansion at chromosome 3q26.2 identified by a CAG/CTG repeat expansion detection array.Human genetics · 2006Article
- A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes I: general principles and overview.Human genetics · 2006Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTo date, 35 human diseases, some of which also exhibit anticipation, have been associated with unstable repeats. Anticipation has been reported in a number of diseases in which repeat expansion may have a role in etiology. Despite the growing importance of unstable repeats in disease, currently no resource exists for the prioritization of repeats. Here we present Satellog, a database that catalogs all pure 1-16 repeat unit satellite repeats in the human genome along with supplementary data. Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism.
resultsA total of 5,546 such repeats were identified, providing the first indication of many novel polymorphic sites in the genome. Overall, polymorphic repeats were over-represented within 3'-UTR sequence relative to 5'-UTR and coding sequence. Interestingly, we observed that repeat polymorphism within coding sequence is restricted to trinucleotide repeats whereas UTR sequence tolerated a wider range of repeat period polymorphisms. For each pure repeat we also calculate its repeat length percentile rank, its location either within or adjacent to EnsEMBL genes, and its expression profile in normal tissues according to the GeneNote database.
conclusionSatellog provides the ability to dynamically prioritize repeats based on any of their characteristics (i.e. repeat unit, class, period, length, repeat length percentile rank, genomic co-ordinates), polymorphism profile within UniGene, proximity to or presence within gene regions (i.e. cds, UTR, 15 kb upstream etc.), metadata of the genes they are detected within and gene expression profiles within normal human tissues. Unstable repeats associated with 31 diseases were analyzed in Satellog to evaluate their common repeat properties. The utility of Satellog was highlighted by prioritizing repeats for Huntington's disease and schizophrenia. Satellog is available online at http://satellog.bcgsc.ca.
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