NucMap: a database of genome-wide nucleosome positioning map across species

Yongbing Zhao, Jinyue Wang, Fang Liang, Yanxia Liu, Qi Wang, Hao Zhang, Meiye Jiang, Zhewen Zhang, Wenming Zhao, Yiming Bao, Zhang Zhang, Jiayan Wu, Yan Asmann, Rujiao Li, Jingfa Xiao

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species. With a series of functional modules, users can search profile of nucleosome positioning at the promoter region of each gene across all samples and make enrichment analysis on nucleosome positioning data in all genomic regions. Nucleosome browser was built to visualize the profiles of nucleosome positioning. Users can also visualize multiple sources of omics data with the nucleosome browser and make side-by-side comparisons. All processed data in the database are freely available. NucMap is the first comprehensive nucleosome positioning platform and it will serve as an important resource to facilitate the understanding of chromatin regulation.

Original languageEnglish (US)
Pages (from-to)D163-D169
JournalNucleic Acids Research
Volume47
Issue numberD1
DOIs
StatePublished - Jan 8 2019

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Nucleosomes
Genome
Databases
Chromatin
Biological Phenomena
Information Storage and Retrieval
Eukaryota
Genetic Promoter Regions

ASJC Scopus subject areas

  • Genetics

Cite this

Zhao, Y., Wang, J., Liang, F., Liu, Y., Wang, Q., Zhang, H., ... Xiao, J. (2019). NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Research, 47(D1), D163-D169. https://doi.org/10.1093/nar/gky980

NucMap : a database of genome-wide nucleosome positioning map across species. / Zhao, Yongbing; Wang, Jinyue; Liang, Fang; Liu, Yanxia; Wang, Qi; Zhang, Hao; Jiang, Meiye; Zhang, Zhewen; Zhao, Wenming; Bao, Yiming; Zhang, Zhang; Wu, Jiayan; Asmann, Yan; Li, Rujiao; Xiao, Jingfa.

In: Nucleic Acids Research, Vol. 47, No. D1, 08.01.2019, p. D163-D169.

Research output: Contribution to journalArticle

Zhao, Y, Wang, J, Liang, F, Liu, Y, Wang, Q, Zhang, H, Jiang, M, Zhang, Z, Zhao, W, Bao, Y, Zhang, Z, Wu, J, Asmann, Y, Li, R & Xiao, J 2019, 'NucMap: a database of genome-wide nucleosome positioning map across species', Nucleic Acids Research, vol. 47, no. D1, pp. D163-D169. https://doi.org/10.1093/nar/gky980
Zhao Y, Wang J, Liang F, Liu Y, Wang Q, Zhang H et al. NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Research. 2019 Jan 8;47(D1):D163-D169. https://doi.org/10.1093/nar/gky980
Zhao, Yongbing ; Wang, Jinyue ; Liang, Fang ; Liu, Yanxia ; Wang, Qi ; Zhang, Hao ; Jiang, Meiye ; Zhang, Zhewen ; Zhao, Wenming ; Bao, Yiming ; Zhang, Zhang ; Wu, Jiayan ; Asmann, Yan ; Li, Rujiao ; Xiao, Jingfa. / NucMap : a database of genome-wide nucleosome positioning map across species. In: Nucleic Acids Research. 2019 ; Vol. 47, No. D1. pp. D163-D169.
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