Evidence map›Paper›PMID 33268804›Full record

ArticleNature communications2020

Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations.

Olivera Grujic, Tanya N Phung, Soo Bin Kwon, Adriana Arneson, Yuju Lee, Kirk E Lohmueller, Jason Ernst

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Pervasive cryptic selection in the human noncoding genome.bioRxiv : the preprint server for biology · 2026
    Article
  2. Article
  3. Review
  4. The Evolving Story in the Genetic Analysis for Heart Failure.Frontiers in cardiovascular medicine · 2021
    Review
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

7 authors.

Olivera GrujicComputer Science Department, University of California, Los Angeles, Los Angeles, CA, 90095, USA.ORCID 0000-0001-6178-9808
Tanya N PhungInterdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Soo Bin KwonDepartment of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.ORCID 0000-0002-8670-0993
Adriana ArnesonDepartment of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Yuju LeeComputer Science Department, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Kirk E LohmuellerInterdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.ORCID 0000-0002-3874-369X
Jason ErnstComputer Science Department, University of California, Los Angeles, Los Angeles, CA, 90095, USA. jason.ernst@ucla.edu.ORCID 0000-0003-4026-7853

Funding

1/2 Genomic Strategies to Identify High-impact Psychiatric Risk VariantsU01MH105578 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FREIMER, NELSON B., GESCHWIND, DANIEL H · 2014 to 2018
$8.5M
"Ribonomics" of Gene Regulation to predict Innate Immune ResponsesU01HG007912 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BLACK, DOUGLAS L, HOFFMANN, ALEXANDER · 2015 to 2017
$5.8M
Impact of coding and non-coding variation in progressive supranuclear palsyUG3NS104095 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DICKSON, DENNIS WILLIAM, GESCHWIND, DANIEL H · 2017 to 2019
$3.6M
Population genomics of the selective effects of new mutationsR35GM119856 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LOHMUELLER, KIRK · 2016 to 2025
$3.4M
Impact of coding and non-coding variation in progressive supranuclear palsyUH3NS104095 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DICKSON, DENNIS WILLIAM, GESCHWIND, DANIEL H · 2020 to 2021
$2.5M
Deciphering the Relationship between Substance Use and Psychiatric Disorders from Whole Genome Sequencing DataDP1DA044371 · NIDA · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ERNST, JASON · 2017 to 2021
$2.3M
Epigenomic control of RNA splicingR01ES024995 · NIEHS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI HOFFMANN, ALEXANDER, XING, YI · 2014 to 2015
$616k
Biomedical Big Data Training GrantT32CA201160 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI PELLEGRINI, MATTEO · 2015 to 2015
$264k
NCI NIH HHS T32 CA201160NHGRI NIH HHS U01 HG007912NIDA NIH HHS DP1 DA044371NIEHS NIH HHS R01 ES024995NIGMS NIH HHS R35 GM119856NIMH NIH HHS U01 MH105578NINDS NIH HHS UG3 NS104095NINDS NIH HHS UH3 NS104095
6 · The paper itself

Abstract

Annotations of evolutionary sequence constraint based on multi-species genome alignments and genome-wide maps of epigenomic marks and transcription factor binding provide important complementary information for understanding the human genome and genetic variation. Here we developed the Constrained Non-Exonic Predictor (CNEP) to quantify the evidence of each base in the genome being in an evolutionarily constrained non-exonic element from an input of over 60,000 epigenomic and transcription factor binding features. We find that the CNEP score outperforms baseline and related existing scores at predicting evolutionarily constrained non-exonic bases from such data. However, a subset of them are still not well predicted by CNEP. We developed a complementary Conservation Signature Score by CNEP (CSS-CNEP) that is predictive of those bases. We further characterize the nature of constrained non-exonic bases with low CNEP scores using additional types of information. CNEP and CSS-CNEP are resources for analyzing constrained non-exonic bases in the genome.

Indexed as

GenomeIntronsAnimalsBase SequenceEpigenesis, GeneticEvolution, MolecularExonsGene OntologyHumansInvertebratesMolecular Sequence AnnotationProtein BindingSequence AlignmentSequence Homology, Nucleic AcidTranscription FactorsVertebratesTranscription Factors

Identifiers

PMID33268804
PMCPMC7710766

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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.