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Article

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Accepted version

Publication date

2018-01-15

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Please use this identifier to cite or link to this item: https://hdl.handle.net/2445/195704

SiNoPsis: single nucleotide polymorphisms selection and promoter profiling

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https://doi.org/10.1093/bioinformatics/btx570

Abstract

Motivation: The selection of a single nucleotide polymorphism (SNP) using bibliographic methods can be a very time-consuming task. Moreover, a SNP selected in this way may not be easily visualized in its genomic context by a standard user hoping to correlate it with other valuable information. Here we propose a web form built on top of Circos that can assist SNP-centered screening, based on their location in the genome and the regulatory modules they can disrupt. Its use may allow researchers to prioritize SNPs in genotyping and disease studies. Results: SiNoPsis is bundled as a web portal. It focuses on the different structures involved in the genomic expression of a gene, especially those found in the core promoter upstream region. These structures include transcription factor binding sites (for promoter and enhancer signals), histones and promoter flanking regions. Additionally, the tool provides eQTL and linkage disequilibrium (LD) properties for a given SNP query, yielding further clues about other indirectly associated SNPs. Possible disruptions of the aforementioned structures affecting gene transcription are reported using multiple resource databases. SiNoPsis has a simple user-friendly interface, which allows single queries by gene symbol, genomic coordinates, Ensembl gene identifiers, RefSeq transcript identifiers and SNPs. It is the only portal providing useful SNP selection based on regulatory modules and LD with functional variants in both textual and graphic modes (by properly defining the arguments and parameters needed to run Circos). Availability and implementation: SiNoPsis is freely available at https://compgen.bio.ub.edu/SiNoPsis/ Supplementary information: Supplementary data are available at Bioinformatics online.

Subject

Polimorfisme genètic, Genomes

Subject (English)

Genetic polymorphisms, Genomes

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Articles publicats en revistes (Genètica, Microbiologia i Estadística)
Articles publicats en revistes (Fonaments Clínics)
Articles publicats en revistes (IDIBAPS: Institut d'investigacions Biomèdiques August Pi i Sunyer)
Articles publicats en revistes (Institut de Biomedicina (IBUB))
Articles publicats en revistes (Medicina)

Citation

BOLOC, Daniel, et al. SiNoPsis: single nucleotide polymorphisms selection and promoter profiling. Bioinformatics. 2018. Vol. 34, num. 2, pags. 303-305. ISSN 1367-4803. [consulted: 9 of August of 2026]. Available at: https://hdl.handle.net/2445/195704

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