The Encyclopedia of DNA Elements (ENCODE): Data Portal Update

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2017 Nov 11

PMID 29126249

Citations 941

Authors

Carrie A Davis

Benjamin C Hitz

Cricket A Sloan

Esther T Chan

Jean M Davidson

Idan Gabdank

Jason A Hilton

Kriti Jain

Ulugbek K Baymuradov

Aditi K Narayanan

Kathrina C Onate

Keenan Graham

Stuart R Miyasato

Timothy R Dreszer

J Seth Strattan

Otto Jolanki

Forrest Y Tanaka

J Michael Cherry

Affiliations

Soon will be listed here.

Abstract

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/.

Citing Articles

A large-scale benchmark for network inference from single-cell perturbation data.

Chevalley M, Roohani Y, Mehrjou A, Leskovec J, Schwab P Commun Biol. 2025; 8(1):412.

PMID: 40069299 PMC: 11897147. DOI: 10.1038/s42003-025-07764-y.

ITGB5 as a Potential Diagnostic Biomarker for Osteoarthritis.

Hu S, Huang J, Wang W J Musculoskelet Neuronal Interact. 2025; 25(1):86-100.

PMID: 40024232 PMC: 11880847. DOI: 10.22540/JMNI-25-086.

Interpreting mammalian synonymous site conservation in light of the unwanted transcript hypothesis.

Christmas M, Dong M, Meadows J, Kozyrev S, Lindblad-Toh K Nat Commun. 2025; 16(1):2007.

PMID: 40011430 PMC: 11865589. DOI: 10.1038/s41467-025-57179-w.

Differential Gene Expression Analysis of Whole Blood Transcriptome Between Young and Old Border Collie Dogs.

Jonas D, Tatrai K, Rekasi Z, Egyed B, Kubinyi E Vet Sci. 2025; 12(2).

PMID: 40005846 PMC: 11860333. DOI: 10.3390/vetsci12020086.

The role of MKI67 in the regulation of 60S pre-ribosome nucleolar export, transcripts, energy supply, and apoptosis.

Iuchi S, Paulo J bioRxiv. 2025; .

PMID: 39990431 PMC: 11844515. DOI: 10.1101/2025.02.13.638155.

References

Gerstein M, Lu Z, Van Nostrand E, Cheng C, Arshinoff B, Liu T . Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010; 330(6012):1775-87. PMC: 3142569. DOI: 10.1126/science.1196914. View

Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A . Integrative analysis of 111 reference human epigenomes. Nature. 2015; 518(7539):317-30. PMC: 4530010. DOI: 10.1038/nature14248. View

Down T, Piipari M, Hubbard T . Dalliance: interactive genome viewing on the web. Bioinformatics. 2011; 27(6):889-90. PMC: 3051325. DOI: 10.1093/bioinformatics/btr020. View

Dekker J, Belmont A, Guttman M, Leshyk V, Lis J, Lomvardas S . The 4D nucleome project. Nature. 2017; 549(7671):219-226. PMC: 5617335. DOI: 10.1038/nature23884. View

Aken B, Achuthan P, Akanni W, Amode M, Bernsdorff F, Bhai J . Ensembl 2017. Nucleic Acids Res. 2016; 45(D1):D635-D642. PMC: 5210575. DOI: 10.1093/nar/gkw1104. View

Rosenbloom K, Dreszer T, Pheasant M, Barber G, Meyer L, Pohl A . ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 2009; 38(Database issue):D620-5. PMC: 2808953. DOI: 10.1093/nar/gkp961. View

Birney E, Stamatoyannopoulos J, Dutta A, Guigo R, Gingeras T, Margulies E . Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007; 447(7146):799-816. PMC: 2212820. DOI: 10.1038/nature05874. View

Baker M . Reproducibility crisis: Blame it on the antibodies. Nature. 2015; 521(7552):274-6. DOI: 10.1038/521274a. View

Rehm H, Berg J, Brooks L, Bustamante C, Evans J, Landrum M . ClinGen--the Clinical Genome Resource. N Engl J Med. 2015; 372(23):2235-42. PMC: 4474187. DOI: 10.1056/NEJMsr1406261. View

10.

Weller M . Quality Issues of Research Antibodies. Anal Chem Insights. 2016; 11:21-7. PMC: 4803150. DOI: 10.4137/ACI.S31614. View

11.

Stamatoyannopoulos J, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert D . An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012; 13(8):418. PMC: 3491367. DOI: 10.1186/gb-2012-13-8-418. View

12.

. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012; 489(7414):57-74. PMC: 3439153. DOI: 10.1038/nature11247. View

13.

Harrow J, Frankish A, Gonzalez J, Tapanari E, Diekhans M, Kokocinski F . GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012; 22(9):1760-74. PMC: 3431492. DOI: 10.1101/gr.135350.111. View

14.

Bujold D, Morais D, Gauthier C, Cote C, Caron M, Kwan T . The International Human Epigenome Consortium Data Portal. Cell Syst. 2016; 3(5):496-499.e2. DOI: 10.1016/j.cels.2016.10.019. View

15.

Sloan C, Chan E, Davidson J, Malladi V, Strattan J, Hitz B . ENCODE data at the ENCODE portal. Nucleic Acids Res. 2015; 44(D1):D726-32. PMC: 4702836. DOI: 10.1093/nar/gkv1160. View

16.

Roy S, Ernst J, Kharchenko P, Kheradpour P, Negre N, Eaton M . Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010; 330(6012):1787-97. PMC: 3192495. DOI: 10.1126/science.1198374. View

17.

Hitz B, Rowe L, Podduturi N, Glick D, Baymuradov U, Malladi V . SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PLoS One. 2017; 12(4):e0175310. PMC: 5389787. DOI: 10.1371/journal.pone.0175310. View

18.

Raney B, Dreszer T, Barber G, Clawson H, Fujita P, Wang T . Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. 2013; 30(7):1003-5. PMC: 3967101. DOI: 10.1093/bioinformatics/btt637. View

19.

Hong E, Sloan C, Chan E, Davidson J, Malladi V, Strattan J . Principles of metadata organization at the ENCODE data coordination center. Database (Oxford). 2016; 2016. PMC: 4792520. DOI: 10.1093/database/baw001. View