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TGD's Supplementary Guidelines for Naming Tetrahymena Genes
Contents
Description
This page defines the terms Gene Name, Standard Name, and Alias, and provides guidelines for naming Tetrahymena genes and for resolving gene naming conflicts if they occur.
What is a gene name?
A Gene Name, for example PDD1 or TIF1, is the name of a gene given to it by a researcher. The "official" Gene Name of a T. thermophila gene is referred to as the Standard Name on a TGD locus page. A Standard Name is a unique gene name that is published in a peer-reviewed journal or submitted to GenBank/EMBL/DDBJ and is the primary accepted name for that gene. Any alternative Gene Name is referred to as an Alias. A Standard Name is adopted on the date it is published, or released by GenBank/EMBL/DDBJ. Standard Names and Aliases are searchable by keywords in TGD. We urge you to include your Gene Name(s) in the abstracts of any relevant papers. This helps the research communitiy identify Tetrahymena Gene Names that are already in use.
Guidelines for naming T. thermophila genes
- Gene Names for T. thermophila generally consist of three letters
(the gene symbol) followed by an integer (e.g. ARP2). In some cases
gene names may not follow this nomenclature. The TTLL genes have been
named to match an ortholog in a different organism, for which there is
an alternate nomenclature guideline. The gene naming guidelines adopted by the Tetrahymena community, published in
Allen, et al. Genetics, 1998, detail a variety of exceptions to this
format that are also
acceptable.
- The Gene Name should be unique for T. thermophila. In
addition, it is a good idea to avoid using Gene Names from other
organisms unless you are naming the Tetrahymena ortholog. When naming your gene consider what other results will be returned when searching for your gene at
public databases, such as TGD, Genbank and Pubmed.
- Before choosing a Gene Name, please search public databases such as TGD, GenBank and PubMed to ensure that no one has published using your gene name or used another gene name for your ORF. (Remember, you can facilitate the community in finding published Gene Names by including your Gene Name in the abstract when you publish.) If, for example, you are interested in using the Gene Name SMC1, you can search TGD by querying "SMC*" in TGD's Quick Search box. You will find that SMC4 already exists and the 3-letter symbol "SMC" is already in use. "SMC" should not be used to describe a different class of genes. We also recommend
you check to see if the gene symbol is currently used by other model
organism communities. Since many of the Tetrahymena gene naming guidelines
mirror those for Saccharomyces, it is often worthwhile to check the
Saccharomyces Genome Database before naming your Tetrahymena
gene.
- The Gene Name should stand for a description of a
phenotype, gene product, or gene function. In addition, we strongly
prefer that a given gene symbol have only one associated description,
i.e., all genes which use a given 3-letter symbol should have a
related phenotype, gene product, or gene function.
- For more
information, please refer to the gene nomenclature guidelines for T. thermophila, published by Allen, et al. Genetics, 1998, and
the Tetrahymena Gene Nomenclature Guidelines. Please note, the use of standardized naming conventions benefits the scientific community by facilitating the indexing and retrieval of gene-related information, and avoids a proliferation of gene names, which can cause confusion in the Tetrahymena literature.
Resolution of gene naming conflicts
In instances where multiple names have been used to describe one gene, or conversely, one name has been applied to
multiple genes, we will work to resolve the nomenclature
conflict. However, please note that TGD typically considers the
gene name first published in a peer-reviewed journal or
released by GenBank to be the Standard Name and it is given priority in most nomenclature conflicts. We recognize that each case is unique, and we strive to choose the most appropriate solution using the following guidelines. We try whenever possible to engage the participation of all interested parties in the resolution of the conflict. We use the following parameters when resolving gene name conflicts:
- Researcher Consensus: We will contact the researchers who have published on the genes involved in the name conflict and request that they come to a resolution that satisfies our Gene Naming guidelines.
- Literature Consensus: In the absence of researcher consensus, we will examine the literature for the number of name usages and the number of different research groups utilizing a particular name usage. If there is a very obvious imbalance, we will favor the more predominant name usage.
- Relevance of the Name: In rare cases where none of the above guidelines apply, we may favor a particular name usage that more accurately describes a phenotype, gene product or gene function.
- Unmapped/Unsequenced genes: This is a special case that applies only to situations where one name has been used for multiple genes. If one of the genes involved in the conflict has never been mapped (physically or genetically) or sequenced, use of the name for that gene may be passed over (even if some of the other guidelines above apply) in favor for a gene known to be mapped or sequenced.
We understand that resolving gene name conflicts causes some pain and inconvenience, especially in the situation where one name has been applied to multiple genes and thus one of these genes will have a completely new name. The TGD curators are happy to check a potential gene name for you. Send us an e-mail message to ciliate-curator@genome.stanford.edu or call us at (650) 724-9959.
Our goal is to serve the Tetrahymena community as a repository of T. thermophila information. As such, we strive to reflect the current community consensus on gene name usages. In order to achieve these goals we need to hear from you! We welcome your questions, comments and suggestions regarding the TGD.
Thanks,
The Staff at TGD
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