Gene Nomenclature Questions
Discovery of new genes, or analysis of current genes sometimes leads to gene nomenclature questions. Here we have listed a few of the more common questions. Please address all comments or questions to firstname.lastname@example.org.
- Where are the Echinobase Gene Nomenclature Guidelines?
- I have found a new gene, how do I name it?
- How do I request a gene name change?
- I have a question about orthologs outside of currently supported Echinoderm species on Echinobase, can you help?
Where are the Echinobase Gene Nomenclature Guidelines?
The Echinobase Gene Nomenclature Guidelines can be found here. These guidelines were created to coincide with the Human Gene Nomenclature guidelines, and have been approved by the Echinobase Nomenclature Committee (ENC). They serve to provide a robust naming schema for echinoderm genes based upon sequence orthology.
What do the Gene Symbol and Gene Name statuses mean?
There are three levels of gene symbol and name curation implemented across the numerous gene pages, corresponding to the level and nature of the curation that has been performed:
Provisional: These are genes whose names and symbols are those generated by NCBI prior to curation through the gene nomenclature guidelines. They can be separated into two types, manually curated identities, and predicted identities. Manual identities are those provided by a user to NCBI prior to processing through the nomenclature guidelines; these will have traditional symbols and names associated with them provided by a user. These are not based on Echinobase gene nomenclature guidelines. Predicted identities are formatted as generic locus IDs for the gene symbol (typically “LOC” followed by the Entrez ID), with the gene name based on the predicted protein product, according to NCBI.
Partially Curated: These genes are a selection of ~2000 genes of interest to users, including those involved in Gene Regulatory Networks, those that were manually curated in earlier assemblies, and those with additional data associated with them in prior versions of Echinobase. These were manually curated with gene symbols and gene names approximating the eventual implementation of the full nomenclature guidelines, based on a bare-bones set of orthology metrics. These gene symbols and names are placeholders for these frequently studied genes until full curation can be completed.
Additional partially curated genes may include those whose Provisional symbols and names are simply locus IDs. These may be appended based upon best BLAST results, and also should not be considered informative of orthology relationships.
Curated: These genes have had their names and symbols updated to represent evolutionary relationships to their human orthologs. By the end of 2020, the full set of Strongylocentrotus purpuratus genes whose names and symbols can be derived by their human orthologs should be curated.
I have found a new gene, how do I name it?
Congratulations! Please keep in mind that the name and symbol must be unique among all species, must conform to our gene nomenclature guidelines, and should be informative as to the function or role of the gene. Please forward as much information as possible to the nomenclature coordinator who will communicate with the ENC to assign the most appropriate name and symbol.
I have a question about orthologs outside of currently supported Echinoderm species on Echinobase, can you help?
Yes we can. We routinely work with other model organism databases to collaborate on gene names. If you have any questions about whether two genes in different species are orthologs, or any other ortholog questions, please let us know.