MethBank
MethBank stores DNA methylome data across a variety of species. MethBank integrates consensus reference methylomes (CRMs) compiled from healthy human samples at different ages, single-base resolution methylomes (SRMs) of both plant and animal species.
Description
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MethBank stores DNA methylome data across a variety of species. MethBank integrates consensus reference methylomes (CRMs) compiled from healthy human samples at different ages, single-base resolution methylomes (SRMs) of both plant and animal species.
metasource: Fairsharing.orgversion: None
MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multiple species and equipping with more enhanced functionalities for data annotation and more friendly web interfaces for data presentation, search and visualization. MethBank 3.0 features large-scale integration of high-quality methylomes, involving 34 consensus reference methylomes derived from a large number of human samples, 336 single-base resolution methylomes from different developmental stages and/or tissues of five plants, and 18 single-base resolution methylomes from gametes and early embryos at multiple stages of two animals. Additionally, it is enhanced by improving the functionalities for data annotation, which accordingly enables systematic identification of methylation sites closely associated with age, sites with constant methylation levels across different ages, differentially methylated promoters, age-specific differentially methylated cytosines/regions, and methylated CpG islands. Moreover, MethBank provides tools to estimate human methylation age online and to identify differentially methylated promoters, respectively. Taken together, MethBank is upgraded with significant improvements and advances over the previous version, which is of great help for deciphering DNA methylation regulatory mechanisms for epigenetic studies.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
https://bigd.big.ac.cn/methbank/Webpage
More detailed information about this field from each metasource.
https://bigd.big.ac.cn/methbank/
metasource: Fairsharing.orgversion: None
http://bigd.big.ac.cn/methbank
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: Creative Commons Attribution 3.0 China Mainland (CC BY 3.0 CN)Licence name
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Creative Commons Attribution 3.0 China Mainland (CC BY 3.0 CN)
metasource: Fairsharing.orgversion: None
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Publications:
Publications
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MethBank 3.0: a database of DNA methylomes across a variety of species
PMID: 29161430
metasource: Fairsharing.org
version: None
http://dx.doi.org/10.1093/nar/gkx1139
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
MethBank 3.0: a database of DNA methylomes across a variety of species
PMID: 29161430
metasource: Fairsharing.org
version: None
http://dx.doi.org/10.1093/nar/gkx1139
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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MethBank 3.0: a database of DNA methylomes across a variety of species
PubMed citations: 24.
24 articles citing: MethBank 3.0: a database of DNA methylomes across a variety of species
Identification of COVID-19-Associated DNA Methylation Variations by Integrating Methylation Array and scRNA-Seq Data at Cell-Type Resolution. PMID:35885892
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. PMID:35325188
GMQN: A Reference-Based Method for Correcting Batch Effects and Probe Bias in HumanMethylation BeadChip. PMID:35069703
The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:34986604
DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database. PMID:34792145
EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. PMID:34718752
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. PMID:34718731
ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms. PMID:34664666
scMethBank: a database for single-cell whole genome DNA methylation maps. PMID:34570235
Novel DNA methylation loci and genes showing pleiotropic association with Alzheimer's dementia: a network Mendelian randomization analysis. PMID:34461811
VDAC Genes Expression and Regulation in Mammals. PMID:34421651
Genome Warehouse: A Public Repository Housing Genome-scale Data. PMID:34175476
ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs. PMID:34050762
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. PMID:33937763
MethHC 2.0: information repository of DNA methylation and gene expression in human cancer. PMID:33270889
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. PMID:33175170
HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis. PMID:32660516
Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate. PMID:32398676
Database Resources of the National Genomics Data Center in 2020. PMID:31702008
EWAS Data Hub: a resource of DNA methylation array data and metadata. PMID:31584095
A method for identifying allele-specific hydroxymethylation. PMID:31533538
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. PMID:30364969
NucMap: a database of genome-wide nucleosome positioning map across species. PMID:30335176 - http://dx.doi.org/10.1093/nar/gkx1139
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dna methylation
metasource: Fairsharing.org
version: None
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
coding and non-coding dna
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
dna methylation
metasource: Fairsharing.orgversion: None
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
coding and non-coding dna
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
dna methylation nucleic acid sequence coding and non-coding dna
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