ArticlePLoS computational biology2007
A survey of genomic properties for the detection of regulatory polymorphisms.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 26 citations in OpenAlex.
- CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2020Article
- CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.BMC bioinformatics · 2019Article
- Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants.Human mutation · 2016Article
- Determining causality and consequence of expression quantitative trait loci.Human genetics · 2014Review
- Article
- Identification of candidate transcription factor binding sites in the cattle genome.Genomics, proteomics & bioinformatics · 2013Article
- Exploring functional variant discovery in non-coding regions with SInBaD.Nucleic acids research · 2013Article
- Article
- Identification of cis-regulatory sequence variations in individual genome sequences.Genome medicine · 2011Article
- Prediction of functional regulatory SNPs in monogenic and complex disease.Human mutation · 2011Article
- Rare and common regulatory variation in population-scale sequenced human genomes.PLoS genetics · 2011Article
- Human variation in short regions predisposed to deep evolutionary conservation.Molecular biology and evolution · 2010Article
- Bioinformatic tools for identifying disease gene and SNP candidates.Methods in molecular biology (Clifton, N.J.) · 2010Review
- EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.Genome biology · 2009Article
- Predicting functional regulatory polymorphisms.Bioinformatics (Oxford, England) · 2008Article
- In silico detection of sequence variations modifying transcriptional regulation.PLoS computational biology · 2008Article
- ORegAnno: an open-access community-driven resource for regulatory annotation.Nucleic acids research · 2008Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Advances in the computational identification of functional noncoding polymorphisms will aid in cataloging novel determinants of health and identifying genetic variants that explain human evolution. To date, however, the development and evaluation of such techniques has been limited by the availability of known regulatory polymorphisms. We have attempted to address this by assembling, from the literature, a computationally tractable set of regulatory polymorphisms within the ORegAnno database (http://www.oreganno.org). We have further used 104 regulatory single-nucleotide polymorphisms from this set and 951 polymorphisms of unknown function, from 2-kb and 152-bp noncoding upstream regions of genes, to investigate the discriminatory potential of 23 properties related to gene regulation and population genetics. Among the most important properties detected in this region are distance to transcription start site, local repetitive content, sequence conservation, minor and derived allele frequencies, and presence of a CpG island. We further used the entire set of properties to evaluate their collective performance in detecting regulatory polymorphisms. Using a 10-fold cross-validation approach, we were able to achieve a sensitivity and specificity of 0.82 and 0.71, respectively, and we show that this performance is strongly influenced by the distance to the transcription start site.
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