ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs

We present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events. ANANASTRA accepts a list of dbSNP IDs or a VCF file and reports allele-specific binding (ASB) sites of pa...

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Autores principales: Boytsov, Alexandr, Abramov, Sergey, Aiusheeva, Ariuna Z, Kasianova, Alexandra M, Baulin, Eugene, Kuznetsov, Ivan A, Aulchenko, Yurii S, Kolmykov, Semyon, Yevshin, Ivan, Kolpakov, Fedor, Vorontsov, Ilya E, Makeev, Vsevolod J, Kulakovskiy, Ivan V
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252736/
https://www.ncbi.nlm.nih.gov/pubmed/35446421
http://dx.doi.org/10.1093/nar/gkac262
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author Boytsov, Alexandr
Abramov, Sergey
Aiusheeva, Ariuna Z
Kasianova, Alexandra M
Baulin, Eugene
Kuznetsov, Ivan A
Aulchenko, Yurii S
Kolmykov, Semyon
Yevshin, Ivan
Kolpakov, Fedor
Vorontsov, Ilya E
Makeev, Vsevolod J
Kulakovskiy, Ivan V
author_facet Boytsov, Alexandr
Abramov, Sergey
Aiusheeva, Ariuna Z
Kasianova, Alexandra M
Baulin, Eugene
Kuznetsov, Ivan A
Aulchenko, Yurii S
Kolmykov, Semyon
Yevshin, Ivan
Kolpakov, Fedor
Vorontsov, Ilya E
Makeev, Vsevolod J
Kulakovskiy, Ivan V
author_sort Boytsov, Alexandr
collection PubMed
description We present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events. ANANASTRA accepts a list of dbSNP IDs or a VCF file and reports allele-specific binding (ASB) sites of particular transcription factors or in specific cell types, highlighting those with ASBs significantly enriched at SNPs in the query list. ANANASTRA is built on top of a systematic analysis of allelic imbalance in ChIP-Seq experiments and performs the ASB enrichment test against background sets of SNPs found in the same source experiments as ASB sites but not displaying significant allelic imbalance. We illustrate ANANASTRA usage with selected case studies and expect that ANANASTRA will help to conduct the follow-up of GWAS in terms of establishing functional hypotheses and designing experimental verification.
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spelling pubmed-92527362022-07-05 ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs Boytsov, Alexandr Abramov, Sergey Aiusheeva, Ariuna Z Kasianova, Alexandra M Baulin, Eugene Kuznetsov, Ivan A Aulchenko, Yurii S Kolmykov, Semyon Yevshin, Ivan Kolpakov, Fedor Vorontsov, Ilya E Makeev, Vsevolod J Kulakovskiy, Ivan V Nucleic Acids Res Web Server Issue We present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events. ANANASTRA accepts a list of dbSNP IDs or a VCF file and reports allele-specific binding (ASB) sites of particular transcription factors or in specific cell types, highlighting those with ASBs significantly enriched at SNPs in the query list. ANANASTRA is built on top of a systematic analysis of allelic imbalance in ChIP-Seq experiments and performs the ASB enrichment test against background sets of SNPs found in the same source experiments as ASB sites but not displaying significant allelic imbalance. We illustrate ANANASTRA usage with selected case studies and expect that ANANASTRA will help to conduct the follow-up of GWAS in terms of establishing functional hypotheses and designing experimental verification. Oxford University Press 2022-04-21 /pmc/articles/PMC9252736/ /pubmed/35446421 http://dx.doi.org/10.1093/nar/gkac262 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Web Server Issue
Boytsov, Alexandr
Abramov, Sergey
Aiusheeva, Ariuna Z
Kasianova, Alexandra M
Baulin, Eugene
Kuznetsov, Ivan A
Aulchenko, Yurii S
Kolmykov, Semyon
Yevshin, Ivan
Kolpakov, Fedor
Vorontsov, Ilya E
Makeev, Vsevolod J
Kulakovskiy, Ivan V
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
title ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
title_full ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
title_fullStr ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
title_full_unstemmed ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
title_short ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
title_sort ananastra: annotation and enrichment analysis of allele-specific transcription factor binding at snps
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252736/
https://www.ncbi.nlm.nih.gov/pubmed/35446421
http://dx.doi.org/10.1093/nar/gkac262
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