Documentation

What is EWAS Open Platform?

With the explosive growth of epigenome-wide association studies (EWAS), a large amount of data and knowledge related to EWAS have been accumulated. Although these data hold great potential for clinical translation, a standardized platform for data archiving, retrieving and exploration is indispensable. For this reason, we updated the existing data resources, EWAS Atlas (Nucleic Acids Res 2019, https://ngdc.cncb.ac.cn/ewas/atlas) and EWAS Data Hub (Nucleic Acids Res 2020, https://ngdc.cncb.ac.cn/ewas/datahub), and proposed EWAS Toolkit (https://ngdc.cncb.ac.cn/ewas/toolkit), an online tool for downstream analysis of EWAS result. Focusing on EWAS research, these three resources provide knowledge, data and tools respectively. More importantly, the quality and functionality for each component are enhanced by cross-linking information from each other. To this end, we present EWAS Open Platform, an integrated one-stop analysis platform for EWAS research.

EWAS Open Platform pipeline


EWAS Open Platform aims to integrate large, diverse and continually arriving EWAS data. There are three parts in this major release:
1. As a curated knowledgebase of EWAS, EWAS Atlas (updated) systematically curated and integrated 617,018 high-quality EWAS associations reported in 910 articles (as of June 15, 2021), involving 193 tissues/cell types, 618 traits and 35,598 genes.
2. As a normalized data portal of EWAS, EWAS Data Hub (updated) integrates DNA methylation data of 115,852 samples from public sources and standardizes the metadata of each sample via a specific data normalization procedure. These data cover 925 different types of tissues and cells, as well as 528 different diseases.
3. Taking advantage of integrated knowledge and data in EWAS Atlas, EWAS Data Hub, and Roadmap Epigenomics Project, EWAS Toolkit is newly developed to provides an online analysis platform for EWAS downstream analysis which includes trait enrichment, genomic location enrichment, GO & KEGG enrichment, chromatin state & histone modification enrichment, tissue methylation, expression regulation and motif enrichment. It provides a one-stop solution for downstream analysis of EWAS and requires no bioinformatics background.

EWAS Atlas

EWAS Atlas, a curated knowledgebase of EWAS. As one of core resources in the National Genomics Data Center of China, EWAS Atlas is devoted to providing a comprehensive collection of high-quality EWAS associations in support of systematic investigations of complex molecular mechanisms associated with different biological traits. Unlike extant data-oriented epigenetic resources, EWAS Atlas features manual curation of EWAS knowledge from extensive publications and accordingly incorporates a large number of high-quality EWAS data and a diversity of traits and ontology entities. EWAS Atlas provides open access to all curated data and thus would serve as a valuable resource for the global research community.
More details about EWAS Atlas are in EWAS Atlas documentation

EWAS Data Hub

To provide the epigenetic research community with a unified data repository that enables data sharing across EWAS, we develop EWAS Data Hub, a public repository that integrates DNA methylation array data (including 450K and 850K in current version) and comprehensive metadata from various data source (GEO, TCGA, ENCODE and ArrayExpress) based on a standard pipeline to minimize batch effects from distinct sources. Besides, taking advantage of big and high quality data, abundant of baseline data on different tissues and conditions are also provided in EWAS Data Hub.
More details about EWAS Data Hub are in EWAS Data Hub documentation

EWAS Toolkit

Taking advantage of integrated knowledge and data in EWAS Atlas, EWAS Data Hub, and Roadmap Epigenomics Project, EWAS Toolkit is newly developed to provides an online analysis platform for EWAS downstream analysis which includes trait enrichment, genomic location enrichment, GO & KEGG enrichment, chromatin state & histone modification enrichment, tissue methylation, expression regulation and motif enrichment. It provides a one-stop solution for downstream analysis of EWAS and requires no bioinformatics background.
More details about EWAS Toolkit are in EWAS toolkit documentation

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