Gene/Protein Nomenclature Guidelines and Requirements for BOR Authors:

1. 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• Sometimes the approved gene/protein name or symbol is no longer valid.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 OCT-4)...". Thereafter, use the correct symbol and not the previous designation.

2. Guidelines for Specific Species

Mouse/Rat/Chicken

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

• (mouse, rat, and chicken) http://www.informatics.jax.org/
• (dedicated to rat) http://rgd.mcw.edu/

General nomenclature rules (applicable to mouse, rat, and chicken):

• Full gene names are not in italics and Greek symbols are NEVER used
  • eg: insulin-like growth factor 1
    
• Gene symbols
  • Greek symbols are never used
  • hyphens are almost never used
  • gene symbols are italicized, first letter upper case all the rest lower case
    • eg: Igf1 (italicized)
• Proteins designations
  • same as the gene symbol, but not italicized and all upper case
    • eg: IGF1
• mRNA and cDNA use the gene symbol and formatting conventions
  • eg: "... levels of Igf1 (italicized) mRNA increased when..."
    
• Mutant alleles should be defined when first mentioned
  • eg: Igf1^tm1Arge/Igf1^tm1Arge (italicized) is one of several knockout alleles of Igf1 (italicized)
    • All letters and numbers are italicized and the allelic designation (tm1Arge) is a superscript
    • After initial specification, the homozygous KO can be indicated as Igf1^-/- (all in italics and -/- as superscript); the heterozygote is Igf1^+/- etc.

For more details on these nomenclature conventions, see:

• MGI Nomenclature page: http://www.informatics.jax.org/mgihome/nomen/index.shtml
• MGI Quick Guide for Genes: http://www.informatics.jax.org/mgihome/nomen/short_gene.shtml

Human/Non-human primates/Domestic species/and default for everything that is not a mouse, rat, fish, worm, or fly

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

• http://www.genenames.org

General rules:

• Full gene names are not italicized and Greek symbols are NEVER used
  • eg: insulin-like growth factor 1
    
• Gene symbols
  • Greek symbols are never used
  • hyphens are almost never used
  • gene symbols are italicized, all letters are in upper case
    • eg: IGF1 (in italics)
• Proteins designations
  • same as the gene symbol, but not italicized and all upper case
    • eg: IGF1
• mRNA and cDNA use the gene symbol and formatting conventions
  • eg: "... levels of IGF1 (in italics) mRNA increased when..."

Fish (use for all fish)

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

• http://zfin.org/cgi-bin/webdriver?MIval=aa-ZDB_home.apg

General rules:

• Full gene names are italicized, all lower case, NEVER use Greek symbols
  • eg: cyclops (in italics)
• Gene symbols are italicized, all lower case
  • eg: cyc (in italics)
• Protein designations are the same as the gene symbol, but first letter only upper case and not italicized
  • eg: Cyc

Other useful websites:

The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) dedicated to the analysis of protein sequences and structures as well as 2-D PAGE: (http://au.expasy.org/)

OMIM – Online inheritance in Man:
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM)

NCBI – Entrez Gene: provides a unified query environment for genes defined by sequence and/or in NCBI's Map Viewer. You can query on names, symbols, accessions, publications, GO terms, chromosome numbers, E.C. numbers, and many other attributes associated with genes and the products they encode.
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene)

Contact for help in nomenclature, registering gene names, symbols, and alleles:
Lois J Maltais: ljm@informatics.jax.org
Sr. Scientific Curator
Member of International Committee on Standardized Genetic Nomenclature for Mice and the Mouse Genomic Nomenclature Committee (MGNC)
Mouse Genome Informatics (MGI) Resource
The Jackson Laboratory
600 Main St
Bar Harbor, ME 04609
207-288-6429 (Ph), 207-288-6131 (Fax)