NBBC: a non-B DNA burden explorer in cancer.

Abstract

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.

• Authors: Qi Xu, Jeanne Kowalski
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 51 Issue W1 Pg. W357-W364 (07 05 2023) ISSN: 1362-4962 [Electronic] England
• PMID: 37224529 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chemical References

• DNA

Topics

• Humans
• Base Sequence
• DNA (genetics, chemistry)
• G-Quadruplexes
• Neoplasms (genetics)
• Nucleotide Motifs