1. NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species.
- Author
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Nie Z, Zhao Y, Yu S, Mai J, Gao H, Fan Z, Bao Y, Li R, and Xiao J
- Subjects
- Humans, Animals, Software, Chromatin Assembly and Disassembly genetics, Transcription Factors genetics, Transcription Factors metabolism, Binding Sites, DNA Methylation, Histone Code genetics, Nucleosomes genetics, Nucleosomes metabolism, Databases, Genetic
- Abstract
Nucleosome dynamics plays important roles in many biological processes, such as DNA replication and gene expression. NucMap (https://ngdc.cncb.ac.cn/nucmap) is the first database of genome-wide nucleosome positioning maps across species. Here, we present an updated version, NucMap 2.0, by incorporating more species and MNase-seq samples. In addition, we integrate other related omics data for each MNase-seq sample to provide a comprehensive view of nucleosome positioning, such as gene expression, transcription factor binding sites, histone modifications and DNA methylation. In particular, NucMap 2.0 integrates and pre-analyzes RNA-seq data and ChIP-seq data of human-related samples, which facilitates the interpretation of nucleosome positioning in humans. All processed data are integrated into an in-built genome browser, and users can make comprehensive side-by-side analyses. In addition, more online analytical functions are developed, which allows researchers to identify differential nucleosome regions and explore potential gene regulatory regions. All resources are open access with a user-friendly web interface., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
- Published
- 2024
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