ArticleGenome research2004
Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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The trial behind it
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
52 citing papers in PubMed.
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- Pharmacogenetic effect of an endothelin-1 haplotype on response to bucindolol therapy in chronic heart failure.Pharmacogenetics and genomics · 2009Trial
- Impact of genetic variations in ADORA2A gene on depression and symptoms: a cross-sectional population-based study.Purinergic signalling · 2019Article
- Genetic insights into juvenile idiopathic arthritis derived from deep whole genome sequencing.Scientific reports · 2017Article
- Article
- A simple repeat polymorphism in the MITF-M promoter is a key regulator of white spotting in dogs.PloS one · 2014Article
- Genetic variants of MARCO are associated with susceptibility to pulmonary tuberculosis in a Gambian population.BMC medical genetics · 2013Article
- Do regulatory regions matter in FOXG1 duplications?European journal of human genetics : EJHG · 2013Article
- An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury.BMC genomics · 2013Article
- Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder.Genome research · 2013Article
- Functional variants in NFKBIE and RTKN2 involved in activation of the NF-κB pathway are associated with rheumatoid arthritis in Japanese.PLoS genetics · 2012Article
- LIM domain only 2 protein expression, LMO2 germline genetic variation, and overall survival in diffuse large B-cell lymphoma in the pre-rituximab era.Leukemia & lymphoma · 2012Article
- Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2012Article
- Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers.PLoS computational biology · 2011Article
- An alternative approach to multiple genome comparison.Nucleic acids research · 2011Article
- Transcriptional regulation of the human P450 oxidoreductase gene: hormonal regulation and influence of promoter polymorphisms.Molecular endocrinology (Baltimore, Md.) · 2011Article
- Current concepts of follicle-stimulating hormone receptor gene regulation.Biology of reproduction · 2011Review
- Combinatorial motif analysis of regulatory gene expression in Mafb deficient macrophages.BMC systems biology · 2011Article
- Long range regulation of human FXN gene expression.PloS one · 2011Article
- Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications.International journal of molecular epidemiology and genetics · 2011Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
We generalize the computation of the Regulatory Potential (RP) score from two-way alignments of human and mouse to three-way alignments of human, mouse, and rat. This requires overcoming technical challenges that arise because the complexity of the models underlying the score increases exponentially with the number of species. Despite the close evolutionary proximity of rat to mouse, we find that adding the rat sequence increases our ability to predict genomic sites that regulate gene transcription. A variant of the RP scoring scheme that accounts for local variation in neutral mutational patterns further improves our predictions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.