ArticleBioinformatics (Oxford, England)2015
atSNP: transcription factor binding affinity testing for regulatory SNP detection.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers, 1 of them a synthesis that pooled it.
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Who cites it
66 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Association between an AMH promoter polymorphism and serum AMH levels in PCOS patients.Human reproduction (Oxford, England) · 2022Pooled it
- Genome-wide association studies of survival in 1520 cancer patients treated with bevacizumab-containing regimens.International journal of cancer · 2022Trial
- Dynamic neuro-immune regulation of psychiatric risk loci in human neurons.Nature communications · 2026Article
- FABIAN-variant 2026: improved prediction of the effects of DNA variants on transcription factor binding.Nucleic acids research · 2026Article
- BMI-genome interactions regulate global gene expression with emphasis in brain and gut.Cell genomics · 2026Article
- SEMPLR: an R package for transcription factor binding prediction.Bioinformatics (Oxford, England) · 2026Article
- Motif grammar and transcriptional programs decouple CTCF binding from nucleosome phasing to control cell-type-specific chromatin insulation.Cell reports · 2026Article
- ceQTL: a co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation.Briefings in bioinformatics · 2026Article
- CanASM: a comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer.BMC genomics · 2025Article
- Identifying deleterious noncoding variation through gain and loss of CTCF binding activity.American journal of human genetics · 2025Article
- SNPeBoT: a tool for predicting transcription factor allele specific binding.BMC bioinformatics · 2025Article
- Identification of Schizophrenia-Risk Regulatory Variant rs1399178 in the Non-coding Region With Its Impact on NRF1 Binding.CNS neuroscience & therapeutics · 2025Article
- Association of Cytotoxic T-Lymphocyte Antigen-4 (International journal of molecular sciences · 2024Article
- Multi-omic human pancreatic islet endoplasmic reticulum and cytokine stress response mapping provides type 2 diabetes genetic insights.Cell metabolism · 2024Article
- A statistical approach for identifying single nucleotide variants that affect transcription factor binding.iScience · 2024Article
- Common variation in a long non-coding RNA gene modulates variation of circulating TGF-β2 levels in metastatic colorectal cancer patients (Alliance).BMC genomics · 2024Article
- Integrative annotation scores of variants for impact on RNA binding protein activities.Bioinformatics (Oxford, England) · 2024Article
- Comparative analysis of models in predicting the effects of SNPs on TF-DNA binding using large-scale in vitro and in vivo data.Briefings in bioinformatics · 2024Article
- Candidate Genes for IgA Nephropathy in Pediatric Patients: Exome-Wide Association Study.International journal of molecular sciences · 2023Article
- Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer's disease brains.Cell & bioscience · 2023Article
6 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
motivationGenome-wide association studies revealed that most disease-associated single nucleotide polymorphisms (SNPs) are located in regulatory regions within introns or in regions between genes. Regulatory SNPs (rSNPs) are such SNPs that affect gene regulation by changing transcription factor (TF) binding affinities to genomic sequences. Identifying potential rSNPs is crucial for understanding disease mechanisms. In silico methods that evaluate the impact of SNPs on TF binding affinities are not scalable for large-scale analysis.
resultsWe describe A: ffinity T: esting for regulatory SNP: s (atSNP), a computationally efficient R package for identifying rSNPs in silico. atSNP implements an importance sampling algorithm coupled with a first-order Markov model for the background nucleotide sequences to test the significance of affinity scores and SNP-driven changes in these scores. Application of atSNP with >20 K SNPs indicates that atSNP is the only available tool for such a large-scale task. atSNP provides user-friendly output in the form of both tables and composite logo plots for visualizing SNP-motif interactions. Evaluations of atSNP with known rSNP-TF interactions indicate that SNP is able to prioritize motifs for a given set of SNPs with high accuracy. AVAILABILITY AND IMPLEMENTATION: https://github.com/keleslab/atSNP. CONTACT: keles@stat.wisc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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