Documentation

What is EWAS Atlas?

EWAS Atlas is used as a knowledgebase of epigenome-wide association studies (EWAS), which not only provides data from published EWAS, but also provides a user-friendly filter for effective retrieval of traits of interest. Moreover, based off of data from EWAS Atlas, a traits enrichment tool was developed to explore the relationshipw between traits or between traits and DNA methylation.

Eligibility criteria

Study
Genome-wide methylation profiles are eligible for integration into EWAS if they meet the following criteria:
  • Based on 850K, 450K and 27K platforms
  • With available differentially methylated position (DMP)
  • EWAS for human traits
Association
  • The p-value is less than 1.0e-4 or q-value less than 0.05.
    (If a study perform genome-wide analysis for initial cohorts and then validate the identified DMP through pyrosequencing, the p-value from initial stage will be reported. For the meta-analysis, the combined p-value was used. If a study does not report a combined p-value, the p-value from the largest sample size will be reported as long as the initial and replication samples each show an association of p < 1.0e-4.)
  • If a study has a p value cutoff less than 1.0e-4 and only provides associations corresponded to their cutoff, all provided associations are recorded.
  • For studies without p-values, all significantly DMP reported in those studies are recorded.

Data structure

Panel Field Description Is it useful?
Publication PMID PubMed ID and links 0   0
Title titles of publications 0   0
Year published year 0   0
Journal published journal 0   0
Citation Citations were extracted from Europe PMC (update per month). 0   0
Datasets Datasets and their links are sourced from the article. 0   0
Study Trait The traits reported in the studies. 0   0
Ontology The reported traits were first mapped to terms from the Experimental Factor Ontology (EFO) automatically by using API provided by ZOOMA and further checked by curators. 0   0
Case/Control group Descriptions of case and control groups. For regression analysis, case group is the description of reported trait. 0   0
#Associations total number of associations reported by studies 0   0
#Cohorts total number of cohorts reported by studies 0   0
Source tissues or cell lines used in studies 0   0
Gene Gene ID gene symbols and ensembl gene ID 0   0
Location genomic position including chr, strand and pos 0   0
Expression gene expression levels in different tissues, data from GTExPortal 0   0
#Association total number of associations related to this gene 0   0
Promoter/Body percentages of associations on promoter or gene body 0   0
Correlations percentages of DNA hyper-/hypo- methylation 0   0
#Related Traits total number of traits related to this gene 0   0
Most Related traits (#Associations) traits are most related to this gene and corresponding number of associations 0   0
Probe Probe ID probe ID in methylation beadchip 0   0
#Studies total number of studies reported this probe 0   0
Correlations percentages of DNA hyper-/hypo- methylation 0   0
Location chr and genomic position 0   0
Related genes (transcript: pos to TSS) For each probe on 850K/450K/27K, the associated transcripts from GENCODE (Release 28) were identified. 0   0
CpG Islands CpG island relations (island, shore, shelf, open sea) 0   0
Related traits all traits related to this probe 0   0
Trait Trait names of traits 0   0
Type trait type (cancer, non-cancer disease, phenotype, environmental factor and behavior) 0   0
#Publications total number of publications for this trait 0   0
#Studies total number of studies for this trait 0   0
#Associations total number of associations related to this trait 0   0
Correlations percentages of DNA hyper-/hypo- methylation 0   0
CpG Island CpG island relations (island, shore, shelf, open sea) 0   0

Trait enrichment tool

Input: Probe ID of 850K/450K/27K
Mode:
  • Global traits mode
    In this mode, a modified Fisher's exact test is used to examine the significance of association between input probes and traits-associated probe lists in EWAS Atlas.
  • Custom traits mode
    Users can customize a set of phenotypic traits, and use modified Fisher's exact test to perform an association analysis between a set of input probes and custom traits associated probes, detecting whether the input probe is associated with the custom phenotypic traits.
Output:
  • Trait: The detected phenotype
  • -log10 (p): The converted p-value of modified fisher test
  • Count: Probes involved in the term
  • Percentage: Involved probes/total probes associated with this trait

How to cite?

EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. Nucleic Acids Res 2019. [PMID=30364969]

Disclaimer

The information on this website is curated from publications and not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have any question about the information contained on this website, please see a health care professional.