ArticleBioinformatics (Oxford, England)2010
is-rSNP: a novel technique for in silico regulatory SNP detection.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed, 155 citations in OpenAlex.
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- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- A statistical approach for identifying single nucleotide variants that affect transcription factor binding.iScience · 2024Article
- Identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data.iScience · 2023Article
- CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes.Human genomics · 2023Article
- Selecting Genetic Variants and Interactions Associated with Amyotrophic Lateral Sclerosis: A Group LASSO Approach.Journal of personalized medicine · 2022Article
- Integrating whole genome sequencing, methylation, gene expression, topological associated domain information in regulatory mutation prediction: A study of follicular lymphoma.Computational and structural biotechnology journal · 2022Article
- GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.PLoS computational biology · 2021Article
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- In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes inInternational journal of molecular sciences · 2021Article
- T-Gene: improved target gene prediction.Bioinformatics (Oxford, England) · 2020Article
- A preliminary computational outputs versus experimental results: Application of sTRAP, a biophysical tool for the analysis of SNPs of transcription factor-binding sites.Molecular genetics & genomic medicine · 2020Article
- Article
- An integrative analysis of genome-wide association study and regulatory SNP annotation datasets identified candidate genes for bipolar disorder.International journal of bipolar disorders · 2020Article
- Predicting the effects of SNPs on transcription factor binding affinity.Bioinformatics (Oxford, England) · 2020Article
- CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2020Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationDetermining the functional impact of non-coding disease-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) is challenging. Many of these SNPs are likely to be regulatory SNPs (rSNPs): variations which affect the ability of a transcription factor (TF) to bind to DNA. However, experimental procedures for identifying rSNPs are expensive and labour intensive. Therefore, in silico methods are required for rSNP prediction. By scoring two alleles with a TF position weight matrix (PWM), it can be determined which SNPs are likely rSNPs. However, predictions in this manner are noisy and no method exists that determines the statistical significance of a nucleotide variation on a PWM score.
resultsWe have designed an algorithm for in silico rSNP detection called is-rSNP. We employ novel convolution methods to determine the complete distributions of PWM scores and ratios between allele scores, facilitating assignment of statistical significance to rSNP effects. We have tested our method on 41 experimentally verified rSNPs, correctly predicting the disrupted TF in 28 cases. We also analysed 146 disease-associated SNPs with no known functional impact in an attempt to identify candidate rSNPs. Of the 11 significantly predicted disrupted TFs, 9 had previous evidence of being associated with the disease in the literature. These results demonstrate that is-rSNP is suitable for high-throughput screening of SNPs for potential regulatory function. This is a useful and important tool in the interpretation of GWAS. AVAILABILITY: is-rSNP software is available for use at: www.genomics.csse.unimelb.edu.au/is-rSNP.
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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 Socratic graph.