Evidence map›Paper›PMID 33758196›Full record

ArticleNature communications2021

Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.

Colin Kern, Ying Wang, Xiaoqin Xu, Zhangyuan Pan, Michelle Halstead, Ganrea Chanthavixay, Perot Saelao, Susan Waters, Ruidong Xiang, Amanda Chamberlain and 11 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
134citing papers in PubMed, 1 pooled it
27.0field-weighted citation impact, top 1% of its field
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

134 citing papers in PubMed, 1 synthesis or guideline pooled it, 288 citations in OpenAlex.

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74 more citing papers are in PubMed but not listed here.

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 at 6 institutions in 3 countries.

Colin KernDepartment of Animal Science, University of California, Davis, Davis, CA, USA.
Ying WangDepartment of Animal Science, University of California, Davis, Davis, CA, USA.
Xiaoqin XuDepartment of Animal Science, University of California, Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0002-9744-1165
Zhangyuan PanDepartment of Animal Science, University of California, Davis, Davis, CA, USA.
Michelle HalsteadDepartment of Animal Science, University of California, Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0003-0168-2704
Ganrea ChanthavixayDepartment of Animal Science, University of California, Davis, Davis, CA, USA.
Perot SaelaoDepartment of Animal Science, University of California, Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0003-1171-9187
Susan WatersDepartment of Animal Science, University of California, Davis, Davis, CA, USA.
Ruidong XiangFaculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia.
Amanda ChamberlainAgriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.ORCID http://orcid.org/0000-0002-9395-1299
Ian KorfGenome Center, University of California, Davis, Davis, CA, USA.
Mary E DelanyDepartment of Animal Science, University of California, Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0001-9901-3597
Hans H ChengUSDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, USA.
Juan F MedranoDepartment of Animal Science, University of California, Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0001-7113-3183
Alison L Van EenennaamDepartment of Animal Science, University of California, Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0003-1562-162X
Chris K TuggleDepartment of Animal Science, Iowa State University, Ames, IA, USA.ORCID http://orcid.org/0000-0002-4229-5316
Catherine ErnstDepartment of Animal Science, Michigan State University, East Lansing, MI, USA.ORCID http://orcid.org/0000-0003-2833-0995
Paul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0002-3897-7955
Gerald QuonDepartment of Molecular and Cellular Biology, University of California, David, Davis, CA, USA.ORCID http://orcid.org/0000-0002-1716-0153
Pablo RossDepartment of Animal Science, University of California, Davis, Davis, CA, USA. pross@ucdavis.edu.ORCID http://orcid.org/0000-0002-3972-3754
Huaijun ZhouDepartment of Animal Science, University of California, Davis, Davis, CA, USA. hzhou@ucdavis.edu.ORCID http://orcid.org/0000-0001-6023-9521
University of California, Davis · USAgriculture Victoria · AUEuropean Bioinformatics Institute · GBIowa State University · USMichigan State University · USThe University of Melbourne · AU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.

Indexed as

Amino Acid MotifsAnimalsAnimals, DomesticCattleChickensChromatin Immunoprecipitation SequencingEnhancer Elements, GeneticEpigenesis, GeneticEpigenomicsGene Expression RegulationGenomeGenome-Wide Association StudyMiceOrgan SpecificityPhylogenyPolymorphism, Single NucleotideTranscription Factors

Identifiers

PMID33758196
PMCPMC7988148
OpenAlexW3138373478

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.