The Encyclopedia of DNA elements (ENCODE): data portal update
Open accessAbstract
The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/.
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Human TBX3 protein binds to E2F7 and E2F8 enhancers.
“Analysis of ChIP-Seq data from the ENCODE database (GSE105374) (33, 34) showed that human TBX3 protein also binds to E2F7 and E2F8 enhancers (SI Appendix, Fig. S3C)”
From Wnt signaling regulates hepatocyte cell division by a transcriptional repressor cascade (2022) · cites this paper as [34]
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- Authors
- Davis, C. A., Hitz, B. C., Sloan, C. A., Chan, E. T., Davidson, J. M., Gabdank, I., Hilton, J. A., Jain, K., Baymuradov, U. K., Narayanan, A. K., Onate, K. C., Graham, K., Miyasato, S. R., Dreszer, T. R., Strattan, J. S., Jolanki, O., Tanaka, F. Y., & Cherry, J. M.
- Affiliations
- Stanford University (US)
- Corresponding author
- Cherry, J Michael
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-11-06
- Volume
- 46
- Issue
- D1
- Pages
- D794-D801
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5753278
- OpenAlex
- W2767826728
- Cited by
- 1,717
- References
- 4
- Citations by year
- 2026: 43 · 2025: 90 · 2024: 145 · 2023: 240 · 2022: 372 · 2021: 384 · 2020: 282 · 2019: 139 · 2018: 18 · 2017: 1
- FWCI
- 51.40
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (U41HG006992, U24HG009397)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- data accessibility, metadata, data provenance, data visualization tools, modENCODE, modern, non-coding DNA, epigenomics
- MeSH terms
- Metadata, Animals, Data Display, DNA, Drosophila melanogaster, Forecasting, Humans, User-Computer Interface, Genome, Human, Caenorhabditis elegans, Genomics, Databases, Genetic, Gene Components, Mice, High-Throughput Nucleotide Sequencing, Datasets as Topic
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