Frequently asked questions

  1. What is the HGNC?
  2. What is PGNC-approved nomenclature and why do we need it?
  3. Where can I find information about existing plant gene symbols?
  4. Do I have to use the approved symbols?
  5. Are there nomenclature committees for other species?
  6. When should I use italics?
  7. How should I refer to the protein encoded by a gene?
  8. How do I perform a search with a term that contains spaces or commas?
  9. What is an alias symbol/name?
  10. What is the difference between a gene symbol and a gene name?
  11. Why isn't punctuation used in a gene symbol?

What is the HGNC?

The Plant Gene Nomenclature Committee is an authority that assigns standardised nomenclature to plant genes. Please see the About page for more information on the committee.

What is PGNC-approved nomenclature and why do we need it?

The PGNC approves both a short-form abbreviation known as a gene symbol, and also a longer and more descriptive name. Each symbol is unique and the committee ensures that each gene is only given one approved gene symbol. This allows for clear and unambiguous reference to genes in scientific communications, and facilitates electronic data retrieval from databases and publications. In preference, symbols also maintain parallel construction for different members of a gene family and can also be used for orthologous genes in other species.

Where can I find information about existing plant gene symbols?

You can search all approved plant gene symbols using the PGNC search facility. Currently the PGNC contains only genes that have been approved for Poplus trichocarpa but more will follow in time.

Do I have to use the approved symbols?

We try to encourage as many researchers as possible to contribute towards development of nomenclature systems in the hope that they will then be more likely to use them. We do realise that not everyone will consistently use approved symbols; but if they are at least mentioned in a publication, it will ensure that the symbol can be used as a search term. This then gives a reference point to facilitate data retrieval in a number of databases including PubMed, NCBI Gene and Phytozome.

Are there nomenclature committees for other species?

Yes, we interact with other nomenclature committees and databases on a regular basis. Please see the following links:

When should I use italics?

The PGNC endorses the use of italicised gene symbols when referring to genes, alleles and RNAs. This distinguishes them from proteins which can be referred to using the non-italicised gene symbol, e.g. the gene CDC45 encodes the CDC45 protein.

How should I refer to the protein encoded by a gene?

Ideally, protein names and symbols would be identical to those used for the gene. However, we are a gene nomenclature committee and do not have any guidelines pertaining to proteins or authority over protein nomenclature. There is a recommendation for the use of italics for gene symbols, and non-italicised letters for the encoded protein; but some journals have editorial policies that prevent this convention from being used, so it is not by any means universal.

How do I perform a search with a term that contains spaces or commas?

If you have a term that you would like to search for within the database that contains a space or a comma, such as "cell division", the term should be double quoted. Anything that is within double quotes will be taken literally as one search term. Without the quotes you will be searching for any entries that contain "cell" and any entries that contain "division".

What is an alias symbol/name?

This is a symbol or name by which a gene has been alternatively referred to in the literature or databases, or which groups it into a known gene family. Aliases are recorded along with the approved symbols and names as part of the gene entry to facilitate database searching.

What is the difference between a gene symbol and a gene name?

Ideally gene symbols are short, memorable and pronounceable, and most gene symbols are short form descriptions or acronyms of the gene name. Names should be brief, specific and convey something about the character or function of the gene product(s), but not attempt to describe everything known.

Why isn't punctuation used in a gene symbol?

Most types of punctuation marks are not permitted in symbols as they can cause difficulty in searches of electronic databases. Use of hyphens may be used but is restricted to certain groups of genes.