Evidence map›Paper›PMID 37172665›Full record

ReviewDevelopmental and comparative immunology2023

Advances in the Xenopus immunome: Diversification, expansion, and contraction.

Dionysia Dimitrakopoulou, Collins N Khwatenge, Christina James-Zorn, Matthieu Paiola, Eleanor Wise Bellin, Yun Tian, Nivitha Sundararaj, Emma J Polak, Leon Grayfer, Daron Barnard and 4 more

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Developmental and comparative immunology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing 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

10 citing papers in PubMed.

  1. Review
  2. Current issues in molecular biology · 2026
    Review
  3. Article
  4. Review
  5. Article
  6. Review
  7. Article
  8. Article
  9. The amphibian immune system.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023
    Review
  10. Biology · 2023
    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

14 authors.

Dionysia DimitrakopoulouDepartment of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
Collins N KhwatengeDepartment of Agriculture and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, USA.
Christina James-ZornXenbase, Division of Developmental Biology, Cincinnti Children's Hospital Medical Center, Cincinnati, OH, USA.
Matthieu PaiolaDepartment of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
Eleanor Wise BellinDepartment of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
Yun TianDepartment of Agriculture and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, USA.
Nivitha SundararajXenbase, Division of Developmental Biology, Cincinnti Children's Hospital Medical Center, Cincinnati, OH, USA.
Emma J PolakBiology Department, Worcester State University, MA, USA.
Leon GrayferDepartment of Biological Sciences, George Washington University, Washington, DC, USA.
Daron BarnardBiology Department, Worcester State University, MA, USA.
Yuko OhtaDepartment of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
Marko HorbNational Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
Yongming SangDepartment of Agriculture and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, USA. Electronic address: ysang@tnstate.edu.
Jacques RobertDepartment of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA. Electronic address: Jacques_Robert@urmc.rochester.edu.

Funding

Xenbase: the Xenopus Model Organism KnowledgebaseP41HD064556 · NICHD · CINCINNATI CHILDRENS HOSP MED CTR · PI PETER D VIZE, Aaron M Zorn · 2010 to 2026
$24.9M
A Xenopus Laevis Research Resource for ImmunologyR24AI059830 · NIAID · UNIVERSITY OF ROCHESTER · PI JACQUES Robert · 2004 to 2026
$7.7M
NIAID NIH HHS R24 AI059830NICHD NIH HHS P41 HD064556
6 · The paper itself

Abstract

Xenopus is a genus of African clawed frogs including two species, X. tropicalis and X. laevis that are extensively used in experimental biology, immunology, and biomedical studies. The availability of fully sequenced and annotated Xenopus genomes is strengthening genome-wide analyses of gene families and transgenesis to model human diseases. However, inaccuracies in genome annotation for genes involved in the immune system (i.e., immunome) hamper immunogenetic studies. Furthermore, advanced genome technologies (e.g., single-cell and RNA-Seq) rely on well-annotated genomes. The annotation problems of Xenopus immunome include a lack of established orthology across taxa, merged gene models, poor representation in gene pages on Xenbase, misannotated genes and missing gene IDs. The Xenopus Research Resource for Immunobiology in collaboration with Xenbase and a group of investigators are working to resolve these issues in the latest versions of genome browsers. In this review, we summarize the current problems of previously misannotated gene families that we have recently resolved. We also highlight the expansion, contraction, and diversification of previously misannotated gene families.

Indexed as

Databases, GeneticGenome-Wide Association StudyAnimalsBase SequenceGenomeHumansXenopus laevisCytokinesDuplicationExpansionImmunomeMajor histocompatibility complexSub-functionalization

Identifiers

PMID37172665
PMCPMC10230362

What OpenQuestion holds

Textmetadata
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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.