Evidence map›Paper›PMID 30598455›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2019

Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy.

Hamutal Arbel, Sumanta Basu, William W Fisher, Ann S Hammonds, Kenneth H Wan, Soo Park, Richard Weiszmann, Benjamin W Booth, Soile V Keranen, Clara Henriquez and 5 more

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing 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

13 citing papers in PubMed.

  1. Review
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  8. Review
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  10. Review
  11. Accurate prediction ofNAR genomics and bioinformatics · 2021
    Article
  12. Article
  13. 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

15 authors.

Hamutal ArbelMolecular Ecosystems Biology Department, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; taly@berkeley.edu bickel@stat.berkeley.edu SECelniker@lbl.gov jbbrown@lbl.gov.
Sumanta BasuMolecular Ecosystems Biology Department, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
William W FisherBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Ann S HammondsBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Kenneth H WanBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Soo ParkBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Richard WeiszmannBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Benjamin W BoothBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Soile V KeranenBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Clara HenriquezBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Omid Shams SolariDepartment of Statistics, University of California, Berkeley, CA 97420.ORCID 0000-0002-7805-6026
Peter J BickelDepartment of Statistics, University of California, Berkeley, CA 97420; taly@berkeley.edu bickel@stat.berkeley.edu SECelniker@lbl.gov jbbrown@lbl.gov.
Mark D BigginBiological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Susan E CelnikerMolecular Ecosystems Biology Department, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; taly@berkeley.edu bickel@stat.berkeley.edu SECelniker@lbl.gov jbbrown@lbl.gov.
James B BrownMolecular Ecosystems Biology Department, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; taly@berkeley.edu bickel@stat.berkeley.edu SECelniker@lbl.gov jbbrown@lbl.gov.

Funding

Using transgenic assays to test, refine and validate the computational modelsP01GM099655 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI BIGGIN, MARK D · 2012 to 2016
$9.6M
Patterned Gene Expression in Drosophila DevelopmentR01GM076655 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI CELNIKER, SUSAN E · 2006 to 2020
$6.8M
Systematic, Genome-Scale Functional Characterization of Conserved smORFsR01HG009352 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI CELNIKER, SUSAN E · 2017 to 2019
$3.0M
Removing statistical bottle-necks in data analysis for the ENCODE ConsortiumU01HG007031 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI BICKEL, PETER J · 2012 to 2015
$1.5M
Nonparametric methods for functional and translational genomicsR00HG006698 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI BROWN, JAMES BENTLEY · 2014 to 2016
$747k
NHGRI NIH HHS R00 HG006698NHGRI NIH HHS R01 HG009352NHGRI NIH HHS U01 HG007031NIGMS NIH HHS P01 GM099655NIGMS NIH HHS R01 GM076655
6 · The paper itself

Abstract

Identifying functional enhancer elements in metazoan systems is a major challenge. Large-scale validation of enhancers predicted by ENCODE reveal false-positive rates of at least 70%. We used the pregrastrula-patterning network of

Indexed as

Drosophila ProteinsSequence Analysis, DNATranscription FactorsAnimalsDrosophila melanogasterEmbryonic DevelopmentEmbryo, NonmammalianEnhancer Elements, GeneticGenome-Wide Association StudyDrosophila ProteinsTranscription FactorsDrosophilaembryo developmentenhancersmachine learningrandom forests

Identifiers

PMID30598455
PMCPMC6338827

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.