Nomenclature Guidelines and Requirements

"NomenBullets"

Biology of Reproduction’s Gene/Protein Nomenclature Guidelines and Requirements


PLEASE NOTE: BOR no longer provides nomenclature editing for accepted papers; it is the authors' responsibility to ensure that their nomenclature is correct prior to publication.


As indicated in the Instructions for Authors, BOR, like many major journals, will no longer publish any paper that is not in full compliance with accepted and standard gene and protein nomenclature. This is to ensure that your paper is clear and precise and has the greatest possible impact. Most publishing databases as well as informatic databases, such as those used by microarray analysis systems and functional interaction systems, now use the standardized nomenclature, so use of correct nomenclature will facilitate incorporation and attribution of your data into these resources.

Be sure that you use correct gene/protein symbols in all sections of your paper, including the Title and Figures. Do not assume that names and symbols that you may have seen used previously in the literature, or perhaps used previously by you, are correct. Please use the species-appropriate databases to check every symbol that you have used throughout your paper, including the Figures, to make sure that (1) the name is correct, (2) the symbol is correct, and (3) the symbol is correctly formatted. Note that gene, transcript, and protein symbols are distinctly formatted, and this facilitates their discrimination in text.

General Guidelines

  • ALWAYS use approved gene/protein names and symbols in your paper (see below)
  • ALWAYS check out every single gene/protein name and symbol in your paper (even if you have seen it published previously and think you know what it is)
  • Sometimes the approved gene/protein name or symbol is different from one that might previously been commonly used but is no longer valid. In these cases, on first mention of the gene/protein, first use the approved designation and then add in parenthesis (previously known as xxx). For example, “… we used antibodies against the POU5F1 protein (previously known as OCT4) …”. Thereafter, use the correct symbol and not the previous designation.

Guidelines for Specific Species

1. Mouse and Rat

1.1 Websites for nomenclature rules and finding gene (and mutant allele) symbols:

1.2 General nomenclature rules (applicable to mouse and rat): Full gene names are not in italics and Greek symbols are NEVER used; e.g., insulin-like growth factor 1, not insulin-like growth factor 1.

1.3 Gene symbols:

  • Greek symbols are not used.
  • hyphens are used only in very specific instances (please refer to the nomenclature guidelines).
  • gene symbols are italicized, first letter upper case all the rest lower case
  • e.g.: Igf1 (italicized)

1.4 Proteins use the same symbol as the gene but are formatted differently: no italics and all upper case; e.g., IGF1.

1.5 Both mRNA and cDNA use the gene symbol and formatting conventions (1.3 above); e.g., “….levels of Igf1 mRNA increased when….”

1.6 Mutant alleles should be defined when first mentioned; e.g., "Igf1tm1Arge/Igf1tm1Arge [the entire symbol is italicized] is one of several knockout alleles of Igf1."

1.6.1 All letters and numbers are italicized and the allelic designation (e.g., tm1Arge) is a superscript

1.6.2 After initial specification, the homozygous KO can be indicated as Igf1 -/- (all in italics and -/- as superscript); the heterozygote is Igf1 +/- etc.

1.7 For more details details on these nomenclature conventions, see:

2. Humans, nonhuman primates, chickens, domestic species, and the default for everything that is not a mouse, rat, fish, worm, frog, or fly

2.1 Website for nomenclature rules and finding gene (and mutant allele) symbols:

2.2 General nomenclature rules: Full gene names are not italicized and Greek symbols are NEVER used; e.g., insulin-like growth factor 1.

2.3 Gene symbols:

  • Greek symbols are never used.
  • hyphens are used only in very specific cases (please refer to the nomenclature guidelines).
  • gene symbols are italicized, all letters are in upper case; e.g., IGF1

2.4 Proteins use the same symbol as the gene but are formatted differently: no italics and all upper case; e.g., IGF1

2.5 All mRNA and cDNA use the gene symbol formatting conventions (see 2.3 above); e.g., “…levels of IGF1 mRNA increased when…”

3. Fish (use for all fish)

3.1 Website for nomenclature rules and gene (and mutant allele) symbols:

3.2 General nomenclature rules:

  • Full gene names are italicized, all lower case, NEVER use Greek symbols; e.g., cyclops
  • Gene symbols are italicized, all lower case; e.g., cyc

3.3 Proteins use the same symbol as the gene but are formatted differently: no italics and the first letter only is capitalized; e.g., Cyc

Other Useful Websites

  • The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.
  • NCBI's Gene provides a unified query environment for genes defined by sequence and/or in NCBI's Map Viewer. Query names, symbols, accessions, publications, GO terms, chromosome numbers, E.C. numbers, or many other attributes associated with genes and the products they encode.
  • OMIM (Online Mendelian Inheritance in Man).
  • Wikipedia’s gene nomenclature page provides a table of species-specific resources with links to the relevant guidelines and databases.

Contact for Help in Registering New Gene Names, Symbols, and Alleles

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