Evidence map›Paper›PMID 41168159›Full record

ArticleNature communications2025

Data navigation on the ENCODE portal.

Meenakshi S Kagda, Bonita Lam, Casey Litton, Corinn Small, Cricket A Sloan, Emma Spragins, Forrest Tanaka, Ian Whaling, Idan Gabdank, Ingrid Youngworth and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.

0numbers the graph read from it
0cells of the map it votes in
54citing 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

54 citing papers in PubMed.

  1. Article
  2. Article
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  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Review
  11. bioRxiv : the preprint server for biology · 2026
    Article
  12. The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026
    Article
  13. Review
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. A sibling study of variation in parental mutation rates.bioRxiv : the preprint server for biology · 2026
    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

29 authors.

Meenakshi S KagdaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-0545-0185
Bonita LamDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Casey LittonDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Corinn SmallDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Cricket A SloanDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-0693-6999
Emma SpraginsDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Forrest TanakaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Ian WhalingDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Idan GabdankDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-5025-5886
Ingrid YoungworthDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
J Seth StrattanDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Jason HiltonDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Jennifer JouDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Jessica AuDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-5043-2245
Jin-Wook LeeDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Kalina AndreevaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Keenan GrahamDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Khine LinDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-5222-2428
Matt SimisonDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Otto JolankiDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-8601-4849
Paul SudDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1667-4694
Pedro AssisDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Philip AdenekanDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Stuart MiyasatoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Weiwei ZhongDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Yunhai LuoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-6948-2042
Zachary MyersDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
J Michael CherryDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-9163-5180
Benjamin C HitzDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA. hitz@stanford.edu.ORCID http://orcid.org/0000-0003-3361-3594

Funding

U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U24-HG009397
6 · The paper itself

Abstract

Spanning two decades, the collaborative ENCODE project aims to identify all the functional elements within human and mouse genomes. To best serve the scientific community, the comprehensive ENCODE data including results from 23,000+ functional genomics experiments, 800+ functional elements characterization experiments and 60,000+ results from integrative computational analyses are available on an open-access data-portal ( https://www.encodeproject.org/ ). The final phase of the project includes data from several novel assays aimed at characterization and validation of genomic elements. In addition to developing and maintaining the data portal, the Data Coordination Center (DCC) implemented and utilised uniform processing pipelines to generate uniformly processed data. Here we report recent updates to the data portal including a redesigned home page, an improved search interface, new custom-designed pages highlighting biologically related datasets and an enhanced cart interface for data visualisation plus user-friendly data download options. A summary of data generated using uniform processing pipelines is also provided.

Indexed as

Databases, GeneticGenome, HumanGenomicsAnimalsComputational BiologyHumansInternetMiceSoftwareUser-Computer Interface

Identifiers

PMID41168159
PMCPMC12575607

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.