Gene nomenclature
Encyclopedia
Gene nomenclature is the scientific naming of genes
, the units of heredity in living organisms. An international committee published recommendations for genetic symbols and nomenclature in 1957. The need to develop formal guidelines for human gene names and symbols was recognized in the 1960s and full guidelines were issued in 1979 (Edinburgh Human Genome Meeting). Several other species-specific research communities (e.g., Drosophila, mouse) have adopted nomenclature standards, as well, and have published them on the relevant model organism
websites and in scientific journals, including the Trends in Genetics Genetic Nomenclature Guide. Scientists familiar with a particular gene family
may work together to revise the nomenclature for the entire set of genes when new information becomes available. For many genes and their corresponding proteins, an assortment of alternate names is in use across the scientific literature and public biological databases, posing a challenge to effective organization and exchange of biological information.
is responsible for providing human gene naming guidelines and approving new, unique human gene names and symbols (short form abbreviations). For some non-human species, model organism databases serve as central repositories of guidelines and help resources, including advice from curators
and nomenclature committees. In addition to species-specific databases, approved gene names and symbols for many species can be located in the National Center for Biotechnology Information's
Entrez Gene database.
The research communities of vertebrate
model organisms have adopted guidelines whereby genes in these species are given, whenever possible, the same names as their human orthologs. The use of prefixes on gene symbols to indicate species (e.g., "Z" for zebrafish) is discouraged. The recommended formatting of printed gene and protein symbols varies between species.
). Italics are not necessary in gene catalogs. Protein designations are the same as the gene symbol, but are not italicised; all letters are in uppercase (SHH). mRNAs and cDNAs use the same formatting conventions as the gene symbol.
See also Bacterial Genetic Nomenclature
Gênes
Gênes is the name of a département of the First French Empire in present Italy, named after the city of Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa. Its capital was Genoa, and it was divided in the arrondissements of Genoa, Bobbio, Novi Ligure, Tortona and...
, the units of heredity in living organisms. An international committee published recommendations for genetic symbols and nomenclature in 1957. The need to develop formal guidelines for human gene names and symbols was recognized in the 1960s and full guidelines were issued in 1979 (Edinburgh Human Genome Meeting). Several other species-specific research communities (e.g., Drosophila, mouse) have adopted nomenclature standards, as well, and have published them on the relevant model organism
Model organism
A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...
websites and in scientific journals, including the Trends in Genetics Genetic Nomenclature Guide. Scientists familiar with a particular gene family
Gene family
A gene family is a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions...
may work together to revise the nomenclature for the entire set of genes when new information becomes available. For many genes and their corresponding proteins, an assortment of alternate names is in use across the scientific literature and public biological databases, posing a challenge to effective organization and exchange of biological information.
Species-specific resources
The HUGO Gene Nomenclature CommitteeHUGO Gene Nomenclature Committee
The HUGO Gene Nomenclature Committee approves a unique and meaningful name for every known human gene based on a query of experts. In addition to a long name, the HGNC also assigns an abbreviation to every gene...
is responsible for providing human gene naming guidelines and approving new, unique human gene names and symbols (short form abbreviations). For some non-human species, model organism databases serve as central repositories of guidelines and help resources, including advice from curators
Biocurator
A biocurator is a professional scientist who collects, annotates, and validates information that is disseminated by biological and model organism databases...
and nomenclature committees. In addition to species-specific databases, approved gene names and symbols for many species can be located in the National Center for Biotechnology Information's
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
Entrez Gene database.
| Species | Guidelines | Database |
|---|---|---|
| Invertebrates | ||
| Fly (Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W... ) |
Genetic nomenclature for Drosophila melanogaster | FlyBase |
| Worm (Caenorhabditis elegans Caenorhabditis elegans Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model... ) |
Genetic Nomenclature for Caenorhabditis elegans | WormBase |
| Plants | ||
| Maize (Zea mays) | A Standard For Maize Genetics Nomenclature | MaizeGDB |
| Thale cress (Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics... ) |
Arabidopsis Nomenclature | The Arabidopsis Information Resource (TAIR). |
| Tree | ||
| Flora | ||
| Mustard (Brassica Brassica Brassica is a genus of plants in the mustard family . The members of the genus may be collectively known either as cabbages, or as mustards... ) |
Standardized gene nomenclature for the Brassica genus (proposed) | |
| Slime molds | ||
| Dictyostelid (Dictyostelium discoideum Dictyostelium discoideum Dictyostelium discoideum is a species of soil-living amoeba belonging to the phylum Mycetozoa. D. discoideum, commonly referred to as slime mold, is a eukaryote that transitions from a collection of unicellular amoebae into a multicellular slug and then into a fruiting body within its lifetime. D... ) |
Nomenclature Guidelines | dictyBase |
| Vertebrates | ||
| Human (Homo sapiens) | Guidelines for Human Gene Nomenclature | HUGO Gene Nomenclature Committee (HGNC) |
| Mouse (Mus musculus), rat (Rattus norvegicus) | Rules for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat | Mouse Genome Informatics (MGI) |
| Frog (Xenopus laevis, X. tropicalis) | Suggested Xenopus Gene Name Guidelines | Xenbase |
| Zebrafish (Danio rerio Danio rerio The zebrafish, Danio rerio, is a tropical freshwater fish belonging to the minnow family of order Cypriniformes. It is a popular aquarium fish, frequently sold under the trade name zebra danio, and is an important vertebrate model organism in scientific research.-Taxonomy:The zebrafish are... ) |
Zebrafish Nomenclature Guidelines | Zebrafish Model Organism Database (ZFIN) |
| Yeast | ||
| Budding yeast (Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes... ) |
SGD Gene Naming Guidelines | Saccharomyces Genome Database |
| Candida (Candida albicans Candida albicans Candida albicans is a diploid fungus that grows both as yeast and filamentous cells and a causal agent of opportunistic oral and genital infections in humans. Systemic fungal infections including those by C... ) |
C. albicans Gene Nomenclature Guide | Candida Genome Database (CGD) |
| Fission yeast (Schizosaccharomyces pombe Schizosaccharomyces pombe Schizosaccharomyces pombe, also called "fission yeast", is a species of yeast. It is used as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measure 3 to 4 micrometres in diameter and 7 to 14 micrometres in length... ) |
Gene Name Registry | Schizosaccharomyces pombe GeneDB |
Vertebrate gene and protein symbol conventions
| Gene and protein symbol conventions ("sonic hedgehog" gene) | ||
| Species | Gene symbol | Protein symbol |
|---|---|---|
| Homo sapiens | SHH | SHH |
| Mus musculus, Rattus norvegicus | Shh | SHH |
| Gallus gallus | SHH | SHH |
| Xenopus laevis, X. tropicalis | shh | shh |
| Danio rerio Danio rerio The zebrafish, Danio rerio, is a tropical freshwater fish belonging to the minnow family of order Cypriniformes. It is a popular aquarium fish, frequently sold under the trade name zebra danio, and is an important vertebrate model organism in scientific research.-Taxonomy:The zebrafish are... |
shh | Shh |
The research communities of vertebrate
Vertebrate
Vertebrates are animals that are members of the subphylum Vertebrata . Vertebrates are the largest group of chordates, with currently about 58,000 species described. Vertebrates include the jawless fishes, bony fishes, sharks and rays, amphibians, reptiles, mammals, and birds...
model organisms have adopted guidelines whereby genes in these species are given, whenever possible, the same names as their human orthologs. The use of prefixes on gene symbols to indicate species (e.g., "Z" for zebrafish) is discouraged. The recommended formatting of printed gene and protein symbols varies between species.
Human
Gene symbols generally are italicised, with all letters in uppercase (e.g., SHH, for sonic hedgehogSonic hedgehog
Sonic hedgehog homolog is one of three proteins in the mammalian signaling pathway family called hedgehog, the others being desert hedgehog and Indian hedgehog . SHH is the best studied ligand of the hedgehog signaling pathway. It plays a key role in regulating vertebrate organogenesis, such as...
). Italics are not necessary in gene catalogs. Protein designations are the same as the gene symbol, but are not italicised; all letters are in uppercase (SHH). mRNAs and cDNAs use the same formatting conventions as the gene symbol.
Mouse and rat
Gene symbols generally are italicised, with only the first letter in uppercase and the remaining letters in lowercase (Shh). Italics are not required on web pages. Protein designations are the same as the gene symbol, but are not italicised, all uppercase letters (SHH).Chicken (Gallus sp.)
Nomenclature generally follows the conventions of human nomenclature. Gene symbols generally are italicised, with all letters in uppercase (e.g., NLGN1, for neuroligin1). Protein designations are the same as the gene symbol, but are not italicised; all letters are in uppercase (NLGN1). mRNAs and cDNAs use the same formatting conventions as the gene symbol.Frog (Xenopus sp.)
Gene symbols are italicised and all letters are in lowercase (shh). Protein designations are the same as the gene symbol, are not italicised, and all letters are in lowercase (shh).Zebrafish
Gene symbols are italicised, with all letters in lowercase (shh). Protein designations are the same as the gene symbol, but are not italicised; the first letter is in uppercase and the remaining letters are in lowercase (Shh).See also Bacterial Genetic Nomenclature
Bacterial Genetic Nomenclature
Bacterial genetic nomenclature is a set of generally accepted rules and conventions used for naming bacterial genes. Standards for were proposed in 1966 by Demerec et al..-General rules:...
External links
- The Council of Science Editors (CSE) - Resources for Genetic and Cytogenetic Nomenclature
- The Protein Naming Utility, a rules database for protein nomenclature