ArticleBMC genomics2012
Large-scale computational identification of regulatory SNPs with rSNP-MAPPER.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 38 citations in OpenAlex.
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- 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
- 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
- Integrating ChIP-seq with other functional genomics data.Briefings in functional genomics · 2018Review
- Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters.BMC genomics · 2018Article
- Pseudoexfoliation syndrome-associated genetic variants affect transcription factor binding and alternative splicing of LOXL1.Nature communications · 2017Article
- SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity.Nucleic acids research · 2017Article
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- Association of vdr, cyp27b1, cyp24a1 and mthfr gene polymorphisms with oral lichen planus risk.Clinical oral investigations · 2016Article
- GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding.Bioinformatics (Oxford, England) · 2016Article
- Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters.BioMed research international · 2016Article
- Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters.Frontiers in immunology · 2016Article
- atSNP: transcription factor binding affinity testing for regulatory SNP detection.Bioinformatics (Oxford, England) · 2015Article
- SNPlice: variants that modulate Intron retention from RNA-sequencing data.Bioinformatics (Oxford, England) · 2015Article
- How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene's Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter.BioMed research international · 2015Article
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1 author at 1 institution in 1 country.
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Abstract
backgroundThe computational analysis of regulatory SNPs (rSNPs) is an essential step in the elucidation of the structure and function of regulatory networks at the cellular level. In this work we focus in particular on SNPs that potentially affect a Transcription Factor Binding Site (TFBS) to a significant extent, possibly resulting in changes to gene expression patterns or alternative splicing. The application described here is based on the MAPPER platform, a previously developed web-based system for the computational detection of TFBSs in DNA sequences.
methodsrSNP-MAPPER is a computational tool that analyzes SNPs lying within predicted TFBSs and determines whether the allele substitution results in a significant change in the TFBS predictive score. The application's simple and intuitive interface supports several usage modes. For example, the user may search for potential rSNPs in the promoters of one or more genes, specified as a list of identifiers or chosen among the members of a pathway. Alternatively, the user may specify a set of SNPs to be analyzed by uploading a list of SNP identifiers or providing the coordinates of a genomic region. Finally, the user can provide two alternative sequences (wildtype and mutant), and the system will determine the location of variants to be analyzed by comparing them.
resultsIn this paper we outline the architecture of rSNP-MAPPER, describing its intuitive and powerful user interface in detail. We then present several examples of the use of rSNP-MAPPER to reproduce and confirm experimental studies aimed at identifying regulatory SNPs in human genes, that show how rSNP-MAPPER is able to detect and characterize rSNPs with high accuracy. Results are richly annotated and can be displayed online or downloaded in a number of different formats.
conclusionsrSNP-MAPPER is optimized for large scale work, allowing for the efficient annotation of thousands of SNPs, and is designed to assist in the genome-wide investigation of transcriptional regulatory networks, prioritizing potential rSNPs for subsequent experimental validation. rSNP-MAPPER is freely available at http://genome.ufl.edu/mapper/.
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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.