Gene nomenclature

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.^[1] The need to develop formal guidelines for human gene names and symbols was recognized in the 1960's and full guidelines were issued in 1979 (Edinburgh Human Genome Meeting).^[2] 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.^[3][4] 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.^[5] For many genes and their corresponding proteins, however, an assortment of alternate names is in use across the scientific literature and public biological databases, thus posing a challenge to effective organization and exchange of biological information.^[6]

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Nomenclature guidelines

Species-specific resources

The HUGO Gene Nomenclature Committee (HGNC) 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.

Invertebrates

• Fly (Drosophila melanogaster): Genetic nomenclature for Drosophila melanogaster at Flybase.
• Worm (Caenorhabditis elegans): Genetic Nomenclature for Caenorhabditis elegans.

Plants

• Maize (Zea mays): A Standard For Maize Genetics Nomenclature at MaizeGDB.
• Thale cress (Arabidopsis thaliana): Arabidopsis Nomenclature at The Arabidopsis Information Resource (TAIR).

Slime molds

• Dictyostelid (Dictyostelium discoideum): Nomenclature Guidelines at dictyBase.

Vertebrates

• Human (Homo sapiens): Guidelines for Human Gene Nomenclature.
• Mouse (Mus musculus) and rat (Rattus norvegicus): Rules for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat at Mouse Genome Informatics (MGI).
• Frog (Xenopus laevis and tropicalis): Suggested Xenopus Gene Name Guidelines at Xenbase.
• Zebrafish (Danio rerio): Zebrafish Nomenclature Guidelines at the Zebrafish Model Organism Database (ZFIN).

Yeast

• Budding yeast (Saccharomyces cerevisiae): SGD Gene Naming Guidelines at Saccharomyces Genome Database.
• Candida (Candida albicans): C. albicans Gene Nomenclature Guide at Candida Genome Database (CGD).
• Fission yeast (Schizosaccharomyces pombe): Gene Naming Guidelines.

Vertebrate gene symbol formatting

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.

Human

Gene symbols generally are italicised, with all letters in uppercase (e.g., SHH, for sonic hedgehog). 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.^[7]

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 letters are in uppercase (SHH).^[8]

Frog (Xenopus sp.)

Gene symbols are not 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 uppercase (SHH).^[9]

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).^[10]

References

1. ^ Report of the International Committee on Genetic Symbols and Nomenclature (1957). Union of International Sci Biol Ser B, Colloquia No. 30.
2. ^ About the HGNC
3. ^ Genetic nomenclature guide (1995). Trends Genet.
4. ^ The Trends In Genetics Nomenclature Guide (1998). Elsevier, Cambridge.
5. ^ Guidelines for Human Gene Nomenclature
6. ^ Fundel and Zimmer (2006). Gene and protein nomenclature in public databases. BMC Bioinformatics 7:372.
7. ^ Guidelines for Human Gene Nomenclature
8. ^ Rules for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat
9. ^ Suggested Xenopus Gene Name Guidelines
10. ^ Zebrafish Nomenclature Guidelines