Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

NucMap (Nucleosome Positioning Map)

General information

Description: NucMap is a database of genome-wide nucleosome positioning map across species. It is dedicated to collecting, analyzing and storing nucleosome positioning data in all organisms. NucMap provides services on querying and visualizing nucleosome positioning information at single nucleotide resolution. Meanwhile, it also provides some enrichment analysis on interested genes or samples.
Year founded: 2018
Last update: 2018-09-12
Version:
Accessibility:
Manual:
Accessible
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Country/Region: China
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Beijing Institute of Genomics, Chinese Academy of Sciences
Address: No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
City: Beijing
Province/State:
Country/Region: China
Contact name (PI/Team): Rujiao Li
Contact email (PI/Helpdesk): lirj@big.ac.cn

Record metadata

Created on: 2019-01-04
Curated by:
Dong Zou [2019-01-08]
Dong Zou [2019-01-04]

Ranking

All databases:
3352/4587 (26.946%)
Gene genome and annotation:
956/1222 (21.849%)
3352
Total Rank
1
Citations
1
z-index

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Publications

30335176
NucMap: a database of genome-wide nucleosome positioning map across species. [PMID: 30335176]
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 W Asmann, Rujiao Li, Jingfa Xiao

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.

Nucleic Acids Res. 2019:47(D1) | 1 Citations (from Europe PMC, 2020-08-01)