NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes

Nucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comprehensive data quality control (QC) assessment and uneven data quality of public data sets....

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Published inBMC bioinformatics Vol. 22; no. 1; pp. 1 - 15
Main Authors Chen, Xiaolan, Yang, Hui, Liu, Guifen, Zhang, Yong
Format Journal Article
LanguageEnglish
Published London BioMed Central Ltd 13.06.2021
BioMed Central
BMC
Subjects
Binding sites
Biological research
Biology, Experimental
Datasets
Design and construction
DNA methylation
Electronic data processing
Filtration
Gene expression
Genetic transcription
Genomes
Mammals
Methods
MNase
Nucleosome
Nucleosomes
Online databases
Quality assessment
Quality control
Structure
Transcription factors
Transcriptional regulation
China
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Summary:Nucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comprehensive data quality control (QC) assessment and uneven data quality of public data sets. The NUCOME is a database focused on filtering qualified nucleosome organization referenced landscapes covering various cell types in human and mouse based on QC metrics. The filtering strategy guarantees the quality of nucleosome organization referenced landscapes and exempts users from redundant data set selection and processing. The NUCOME database provides standardized, qualified data source and informative nucleosome organization features at a whole-genome scale and on the level of individual loci. The NUCOME provides valuable data resources for integrative analyses focus on nucleosome organization. The NUCOME is freely available at http://compbio-zhanglab.org/NUCOME.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-021-04239-9