MethBank 3.0: a database of DNA methylomes across a variety of species

Abstract

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.

HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis

“…Exon and isoform annotations were taken from the file Homo_sapiens.GRCh38.91.gtf that was download from the Ensembl website. The methylation datasets were downloaded from MethBank [50]. The age groups were age0, age2-4, age5-13, age14-16, age17-28, age29-36, age37-42, age43-53, age54-66, age67-75, age76-88, and age89-101.…”

MethHC 2.0: information repository of DNA methylation and gene expression in human cancer

“…Large amounts of methylation data and disease information have been collected, integrated, and made available from many sources such as The Cancer Genome Atlas (TCGA) project, Gene Expression Omnibus (GEO), and databases including iMETHYL ( 15 ), MethBank ( 16 ), DiseaseMeth ( 17 , 18 ), MethyCancer ( 19 ), MethDB ( 20 ), NGSmethDB ( 21 , 22 ), PubMeth ( 23 ) and MENT ( 24 ). Most of these sources are constantly updated, including our previously developed MethHC ( 25 ).…”

“…iMETHYL is a multi-omics database that provides DNA methylation, whole genome, and whole transcriptome data for immune cells ( 15 ). MethBank 3.0 integrates DNA methylomes across various species with an update of data annotation, detailed methylomes of different developmental stages, and an interactive browser ( 16 ). DiseaseMeth has developed a 2.0 version that provides datasets for 88 human diseases in locus-specific and genome-wide form and allows the online automated identification of abnormal DNA methylation in human diseases ( 17 , 18 ).…”

Identification of a new methylation site in the Sept9 promoter region for the diagnosis of hepatocellular carcinoma

“…Важный критерий для выбора опухольспецифических маркеров, используемых для жидкостной биопсии, -их минимальный фоновый уровень в тканях и клетках, вносящих вклад в общий пул ДНК, циркулирующих в биологических жидкостях организма. Поскольку важным источником цДНК плазмы и сыворотки крови являются клетки периферической крови, на следующем этапе отбора мы сравнили уровни метилирования исследуемых локусов по данным базы Methbank [19], которая включает данные о метилировании образцов крови 4577 здоровых доноров разного возраста, а также от 38 до 322 образцов 8 типов нормальных тканей человека.…”