Evidence map›Paper›PMID 37794265›Full record

ReviewNature2023

The status of the human gene catalogue.

Paulo Amaral, Silvia Carbonell-Sala, Francisco M De La Vega, Tiago Faial, Adam Frankish, Thomas Gingeras, Roderic Guigo, Jennifer L Harrow, Artemis G Hatzigeorgiou, Rory Johnson and 11 more

Abstract readReview
In one paragraph

Review in Nature, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.

0numbers the graph read from it
0cells of the map it votes in
106citing 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

106 citing papers in PubMed.

  1. Review
  2. Article
  3. Oral virome in health and disease.Journal of the American Dental Association (1939) · 2026
    Review
  4. Article
  5. Determining the dark proteome.Nature chemical biology · 2026
    Article
  6. The dark genome in cardiovascular medicine.European heart journal · 2026
    Review
  7. Review
  8. Review
  9. Article
  10. Article
  11. Article
  12. Review
  13. Therapeutic peptides and proteins: Status and developments in drug delivery.Journal of controlled release : official journal of the Controlled Release Society · 2026
    Review
  14. Review
  15. Review
  16. Article
  17. Article
  18. Article
  19. Article
  20. Article

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

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

21 authors.

Paulo AmaralINSPER Institute of Education and Research, Sao Paulo, Brazil.
Silvia Carbonell-SalaCentre for Genomic Regulation (CRG), Barcelona, Spain.ORCID 0000-0001-7956-6215
Francisco M De La VegaDepartment of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA.
Tiago FaialNature Genetics, San Francisco, CA, USA.
Adam FrankishEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
Thomas GingerasDepartment of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Roderic GuigoCentre for Genomic Regulation (CRG), Barcelona, Spain.
Jennifer L HarrowCentre for Genomics Research, Discovery Sciences, AstraZeneca, Royston, UK.
Artemis G HatzigeorgiouDepartment of Computer Science and Biomedical Informatics, Universithy of Thessaly, Lamia, Greece.
Rory JohnsonSchool of Biology and Environmental Science, University College Dublin, Dublin, Ireland.ORCID 0000-0003-4607-2782
Terence D MurphyNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0001-9311-9745
Mihaela PerteaCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Kim D PruittNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Shashikant PujarNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Hazuki TakahashiLaboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.ORCID 0000-0001-7315-7349
Igor UlitskyDepartment of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
Ales VarabyouCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.ORCID 0000-0003-1060-7212
Christine A WellsStem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.ORCID 0000-0003-3133-3628
Mark YandellDepartent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.ORCID 0000-0002-9497-4505
Piero CarninciLaboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. piero.carninci@fht.org.ORCID 0000-0001-7202-7243
Steven L SalzbergCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.ORCID 0000-0002-8859-7432

Funding

Single-Cell Biology Shared ResourceP30CA045508 · NCI · COLD SPRING HARBOR LABORATORY · PI John Edward Moses · 1987 to 2026
$118.9M
GENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3M
GENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1M
Computational Methods for Genome Assembly, Transcript Assembly, and Variant DiscoveryR01HG006677 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI SALZBERG, STEVEN L. · 2011 to 2025
$10.7M
Computational Methods for Microbial and Microbiome Sequence AnalysisR35GM130151 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Steven L. Salzberg · 2019 to 2026
$2.9M
Comprehensive Human Expressed Sequences in Brain (CHESS-BRAIN) and their roles in neuropsychiatric illnessR01MH123567 · NIMH · JOHNS HOPKINS UNIVERSITY · PI SALZBERG, STEVEN L. · 2021 to 2025
$2.8M
Intramural NIH HHS Z99 LM999999NCI NIH HHS P30 CA045508NHGRI NIH HHS R01 HG006677NHGRI NIH HHS U24 HG007234NHGRI NIH HHS U41 HG007234NIGMS NIH HHS R35 GM130151NIMH NIH HHS R01 MH123567Wellcome Trust
6 · The paper itself

Abstract

Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.

Indexed as

GenesGenome, HumanMolecular Sequence AnnotationProtein IsoformsHuman Genome ProjectHumansPseudogenesRNAProtein IsoformsRNA

Identifiers

PMID37794265
PMCPMC10575709

What OpenQuestion holds

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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.