When writing a manuscript, it is important to follow general usage and conventions for gene nomenclature to ensure the greatest chance of making it through peer review. With the broadening use of genetic analysis and consideration of genes in more and more areas of science, the appropriate use of gene symbols and notation is becoming a more common question.
Though some journals will request specific formatting when referring to genetic work, there are some standards that fit the general expectations of readers and researchers in the field. Following standard conventions allows both reviewers and readers to understand the intended meaning and follow the research without getting hung up on questions about exactly which gene (or gene product) is being discussed. However, there is one very important caveat to the advice below–always follow what a journal or publisher requests in order to stand the best chance at publication.
Official gene names and symbols
The official names of human genes (and those of other select species) and their accepted gene symbols are available at several websites, including HUGO Gene Nomenclature Committee, NCBI Gene, and OMIM (Online Mendelian Inheritance in Man). Similarly, if you are working with mouse genetics, there is MGI (Mouse Genome Informatics), for rats RGD (Rat Genome Database), and for Drosophila FlyBase. The official gene names do not always match the common gene names, so it is important to also look for aliases. In addition, some names are no longer relevant–the newer genetic designations should be used, but you can note the former name in parentheses for clarity. For example, “y (known previously as x).”
The accepted gene symbols tend to be acronyms or abbreviations but can also be unexpected sequences because of similarities with other, earlier designations. Most of these longer symbols will have shorter, more common aliases. When deciding which name to use for the gene in your paper, be clear and consistent. If the material was provided by a third party, use their designation consistently but also provide the official alias if it is not clear. Also, after choosing the designation you prefer to use, if there is a more common way of referring to the gene, provide that information for readers in order to make your work easy to understand and replicate.
Italicized gene notation
A common mistake made before submission for publication is the misuse of italics in gene notation. Italics are used specifically to denote a gene symbol as a way to differentiate it from the gene product. Proteins are often referred to by the same name or symbol as the gene that encodes them, but protein names are never italicized. Put simply:
-When referring to the genetic element (or genotype), the abbreviation is italicized.
-When referring to the protein (or phenotype), do not use italics.
This means that, when referring to the mRNA, the italicized notation is used, even if the notation is followed by the word “mRNA”. This also needs to be kept in mind when writing about genotypes. The notation is italicized because it is referring to the genetic sequence, often in the context of being knocked out or altered. For example, IL6-/-. However, the fully written out gene name is not italicized unless it is a gene from fish. Some journals specifically outline this rule and offer additional exceptions, so be sure to check their author guidelines and recent articles to verify the style you are expected to follow for full gene names in the species you are working with.
Exceptions to italic gene symbols
Some journals and publishers will request that tables with long lists of gene names not be italicized. This may be due to known issues in the conversion of tables for publication or simply for readability. Regardless of the reason, it is important to follow the directions provided by the journal to have the best chance at publication. If it seems that removing the formatting will confuse readers, use the title of the table or the column heading to make it clear that the notations given are the gene symbols.
A common mistake with italics
A common issue is the confusion of whether to italicize the gene symbol when following it with the word “gene”. When this sentence construction is used, the symbol is then referring to the gene product and should not be italicized.
For example: “IL-6 gene” and “interleukin-6 gene” mean the same thing as “IL6”.
However, “the gene encoding IL-6 (IL6),” can be seen as a confusing exception.
Species variance in gene notation
It is important to keep in mind the variances in gene notation between species. A common mistake is capitalizing all genes when both human and rodent genes are mentioned in the same study. Human gene symbols are denoted in all capital letters, such as TNFA. Rodent and other species’ gene symbols are in lowercase, with only the first letter capitalized, such as Tnfa.
Elements to avoid in gene symbols
Often, there are slight differences between the gene symbols and the abbreviations used for the proteins they encode. An exception is in fish and bacteria, which generally have the same gene and protein notations, varying only by italics. There are also additional exceptions for some species other than humans, such as C. elegans, and these are outlined by the official naming organizations for these species.
In humans, rodents, and most other species, it is important to ensure that gene symbols avoid the use of hyphens, superscript and subscript letters, Greek letters, and Roman numerals.
For example, TNF-α induced protein 6 is encoded by TNFAIP6.
Appropriate gene nomenclature
To sum it all up, when writing your paper, be sure to use accepted gene symbols and/or aliases by double-checking them at the websites noted above or other dedicated databases, such as the Alliance of Genome Resources. Ensure that italics are used only for the gene symbol, not the protein notation, and that the appropriate capitalization is used for the species being studied. Finally, double-check the author guidelines of the journal where you are planning to submit the paper to ensure they don’t have exceptions to the rules that need to be followed.
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