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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...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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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. |
format | Online Article Text |
id | pubmed-9252736 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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