Format

Send to

Choose Destination
Bioinformatics. 2017 Sep 14. doi: 10.1093/bioinformatics/btx570. [Epub ahead of print]

SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling.

Author information

1
Dep. de Medicina, University of Barcelona, Barcelona, Catalonia, Spain. Contact: danielboloc@gmail.com
2
Dep. Fonaments Clínics, Unitat de Farmacologia, University of Barcelona, Barcelona, Catalonia, Spain.
3
Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain.
4
Dep. de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain.
5
Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain.
6
Unitat Esquizofrènia, Hospital Clínic de Barcelona, Barcelona, Catalonia, Spain.
7
Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Barcelona, Catalonia, Spain.

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-centred 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.

Summary:

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).

Supplementary information:

SiNoPsis is freely available at https://compgen.bio.ub.edu/SiNoPsis /.

Supplemental Content

Full text links

Icon for Silverchair Information Systems
Loading ...
Support Center