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SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

Motivation: The vast majority of the many thousands of disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding part of the genome. They are likely to affect regulatory elements, such as enhancers and promoters, rather than the function of a protein. To understand the molecula...

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Detalles Bibliográficos
Autores principales: Arnold, Christian, Bhat, Pooja, Zaugg, Judith B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965630/
https://www.ncbi.nlm.nih.gov/pubmed/27153574
http://dx.doi.org/10.1093/bioinformatics/btw127
Descripción
Sumario:Motivation: The vast majority of the many thousands of disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding part of the genome. They are likely to affect regulatory elements, such as enhancers and promoters, rather than the function of a protein. To understand the molecular mechanisms underlying genetic diseases, it is therefore increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin or transcription factor binding. Results: We developed SNPhood, a user-friendly Bioconductor R package to investigate, quantify and visualise the local epigenetic neighbourhood of a set of SNPs in terms of chromatin marks or TF binding sites using data from NGS experiments. Availability and implementation: SNPhood is publicly available and maintained as an R Bioconductor package at http://bioconductor.org/packages/SNPhood/. Contact: judith.zaugg@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.