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NBBC: a non-B DNA burden explorer in cancer
Alternate (non-B) DNA-forming structures, such as Z-DNA, G-quadruplex, triplex have demonstrated a potential role in cancer etiology. It has been found that non-B DNA-forming sequences can stimulate genetic instability in human cancer genomes, implicating them in the development of cancer and other...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320089/ https://www.ncbi.nlm.nih.gov/pubmed/37224529 http://dx.doi.org/10.1093/nar/gkad379 |
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author | Xu, Qi Kowalski, Jeanne |
author_facet | Xu, Qi Kowalski, Jeanne |
author_sort | Xu, Qi |
collection | PubMed |
description | Alternate (non-B) DNA-forming structures, such as Z-DNA, G-quadruplex, triplex have demonstrated a potential role in cancer etiology. It has been found that non-B DNA-forming sequences can stimulate genetic instability in human cancer genomes, implicating them in the development of cancer and other genetic diseases. While there exist several non-B prediction tools and databases, they lack the ability to both analyze and visualize non-B data within a cancer context. Herein, we introduce NBBC, a non-B DNA burden explorer in cancer, that offers analyses and visualizations for non-B DNA forming motifs. To do so, we introduce ‘non-B burden’ as a metric to summarize the prevalence of non-B DNA motifs at the gene-, signature- and genomic site-levels. Using our non-B burden metric, we developed two analyses modules within a cancer context to assist in exploring both gene- and motif-level non-B type heterogeneity among gene signatures. NBBC is designed to serve as a new analysis and visualization platform for the exploration of non-B DNA, guided by non-B burden as a novel marker. |
format | Online Article Text |
id | pubmed-10320089 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-103200892023-07-06 NBBC: a non-B DNA burden explorer in cancer Xu, Qi Kowalski, Jeanne Nucleic Acids Res Web Server Issue Alternate (non-B) DNA-forming structures, such as Z-DNA, G-quadruplex, triplex have demonstrated a potential role in cancer etiology. It has been found that non-B DNA-forming sequences can stimulate genetic instability in human cancer genomes, implicating them in the development of cancer and other genetic diseases. While there exist several non-B prediction tools and databases, they lack the ability to both analyze and visualize non-B data within a cancer context. Herein, we introduce NBBC, a non-B DNA burden explorer in cancer, that offers analyses and visualizations for non-B DNA forming motifs. To do so, we introduce ‘non-B burden’ as a metric to summarize the prevalence of non-B DNA motifs at the gene-, signature- and genomic site-levels. Using our non-B burden metric, we developed two analyses modules within a cancer context to assist in exploring both gene- and motif-level non-B type heterogeneity among gene signatures. NBBC is designed to serve as a new analysis and visualization platform for the exploration of non-B DNA, guided by non-B burden as a novel marker. Oxford University Press 2023-05-24 /pmc/articles/PMC10320089/ /pubmed/37224529 http://dx.doi.org/10.1093/nar/gkad379 Text en © The Author(s) 2023. 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 Xu, Qi Kowalski, Jeanne NBBC: a non-B DNA burden explorer in cancer |
title | NBBC: a non-B DNA burden explorer in cancer |
title_full | NBBC: a non-B DNA burden explorer in cancer |
title_fullStr | NBBC: a non-B DNA burden explorer in cancer |
title_full_unstemmed | NBBC: a non-B DNA burden explorer in cancer |
title_short | NBBC: a non-B DNA burden explorer in cancer |
title_sort | nbbc: a non-b dna burden explorer in cancer |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320089/ https://www.ncbi.nlm.nih.gov/pubmed/37224529 http://dx.doi.org/10.1093/nar/gkad379 |
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