Evidence map›Paper›PMID 31751002›Full record

ArticleCurrent protocols in bioinformatics2019

The ENCODE Portal as an Epigenomics Resource.

Jennifer Jou, Idan Gabdank, Yunhai Luo, Khine Lin, Paul Sud, Zachary Myers, Jason A Hilton, Meenakshi S Kagda, Bonita Lam, Emma O'Neill and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Current protocols in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

23 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Data navigation on the ENCODE portal.Nature communications · 2025
    Article
  6. Article
  7. Review
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. The ENCODE Uniform Analysis Pipelines.bioRxiv : the preprint server for biology · 2023
    Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors.

Jennifer JouDepartment of Genetics, Stanford University, Stanford, California.
Idan GabdankDepartment of Genetics, Stanford University, Stanford, California.
Yunhai LuoDepartment of Genetics, Stanford University, Stanford, California.
Khine LinDepartment of Genetics, Stanford University, Stanford, California.
Paul SudDepartment of Genetics, Stanford University, Stanford, California.
Zachary MyersDepartment of Genetics, Stanford University, Stanford, California.
Jason A HiltonDepartment of Genetics, Stanford University, Stanford, California.
Meenakshi S KagdaDepartment of Genetics, Stanford University, Stanford, California.
Bonita LamDepartment of Genetics, Stanford University, Stanford, California.
Emma O'NeillDepartment of Genetics, Stanford University, Stanford, California.
Philip AdenekanDepartment of Genetics, Stanford University, Stanford, California.
Keenan GrahamDepartment of Genetics, Stanford University, Stanford, California.
Ulugbek K BaymuradovDepartment of Genetics, Stanford University, Stanford, California.
Stuart R MiyasatoDepartment of Genetics, Stanford University, Stanford, California.
J Seth StrattanDepartment of Genetics, Stanford University, Stanford, California.
Otto JolankiDepartment of Genetics, Stanford University, Stanford, California.
Jin-Wook LeeDepartment of Genetics, Stanford University, Stanford, California.
Casey LittonDepartment of Genetics, Stanford University, Stanford, California.
Forrest Y TanakaDepartment of Genetics, Stanford University, Stanford, California.
Benjamin C HitzDepartment of Genetics, Stanford University, Stanford, California.
J Michael CherryDepartment of Genetics, Stanford University, Stanford, California.

Funding

A Data Coordinating Center for ENCODEU24HG009397 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2017 to 2023
$26.0M
NHGRI NIH HHS U24 HG009397
6 · The paper itself

Abstract

The Encyclopedia of DNA Elements (ENCODE) web portal hosts genomic data generated by the ENCODE Consortium, Genomics of Gene Regulation, The NIH Roadmap Epigenomics Consortium, and the modENCODE and modERN projects. The goal of the ENCODE project is to build a comprehensive map of the functional elements of the human and mouse genomes. Currently, the portal database stores over 500 TB of raw and processed data from over 15,000 experiments spanning assays that measure gene expression, DNA accessibility, DNA and RNA binding, DNA methylation, and 3D chromatin structure across numerous cell lines, tissue types, and differentiation states with selected genetic and molecular perturbations. The ENCODE portal provides unrestricted access to the aforementioned data and relevant metadata as a service to the scientific community. The metadata model captures the details of the experiments, raw and processed data files, and processing pipelines in human and machine-readable form and enables the user to search for specific data either using a web browser or programmatically via REST API. Furthermore, ENCODE data can be freely visualized or downloaded for additional analyses. © 2019 The Authors. Basic Protocol: Query the portal Support Protocol 1: Batch downloading Support Protocol 2: Using the cart to download files Support Protocol 3: Visualize data Alternate Protocol: Query building and programmatic access.

Indexed as

Databases, GeneticAnimalsChromatinDNADNA MethylationEpigenomicsGenome, HumanHumansInternetMetadataMiceSoftwareChromatinDNAdatabaseENCODEepigeneticshuman genomeregulatory elements

Identifiers

PMID31751002
PMCPMC7307447

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.