ArticleBMC genomics2025
Protein-coding genes in humans and model mammals (mouse, rat and pig): gene identifiers and disambiguation of gene nomenclature retrieved from the Ensembl genome browser.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper, 1 of them a synthesis that pooled it.
What it found
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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.
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.
Who cites it
1 citing paper in PubMed, 1 synthesis or guideline pooled it.
- Brain Proteomic Responses to Glucocorticoids and Their Relationship With Transcriptome: A Systematic Meta-Analysis.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Pooled it
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundGene nomenclature contains current official symbols and various numbers of synonyms, which pose a challenge to integrating genomic data and increase the probability that different genes share the same symbol. Therefore, we retrieved identifiers assigned to all protein-coding genes in human, mouse, rat and pig genomes that are available in the Ensembl genome browser (release 113) to assess the number of genes, compare species and identify ambiguous symbols.
resultsOur analysis revealed that the total number of symbols, both official symbols and synonyms, used to identify protein-coding genes ranges from 16,600 in pigs to 64,580 in mice. Furthermore, the gene nomenclature is not complete because there are also genes without an assigned symbol, which indicates gaps in understanding protein-coding genes, especially in pigs. We also found a large number of gene symbols that map to more than one gene. These symbols might complicate the identification of about 10% of rat and mouse genes and 18% of human protein-coding genes. A simple solution for this problem is the usage of stable gene IDs assigned by scientific institutions and committees (Ensembl, NCBI, RGD, HGNC and VGNC) provided that the genomic information associated with these IDs is retrieved directly from proprietary databases containing the most accurate data. Finally, although gene symbols may pose a problem with unequivocal identification of genes, there are instances when no other identifiers are available in the literature. Therefore, we have developed an R script performing search of the Ensembl database and integrating data to provide a single list of updated symbols with annotation about their ambiguity.
conclusionsGene symbols are not always reliable and should be reported together with stable IDs to enable unequivocal identification of genes. Therefore, data containing only gene symbols should be used cautiously to avoid misidentification of genes. A solution for this problem is our R script REgeness that performs a gene symbol update to current official versions combined with identification of ambiguous symbols and retrieval of other IDs from the Ensembl database.
Indexed as
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What OpenQuestion holds
Registered trials
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.