Find official gene symbol and alternative symbols for given gene

The abbreviations, or gene symbols, by which a gene has been known often vary over time. Nomenclature committees exist for a number of organisms. RefSeq Collaborators include nomenclature committees for various genomes for example, the Human Gene Nomenclature Committee. The committee assign official symbols to an organism's genes, and keeps a record of the alternate symbols ("aliases") by which the gene has been known.

Sequence records in archival databases such as GenBank/EMBL/DDBJ do not use a controlled vocabulary, and do not necessarily contain an official gene symbol (or in some cases, any gene symbol). Instead, the records contain the information that was provided by the submitters of the sequence records. Depending on whether, and when, submitters checked with the nomenclature for their organism of study, their sequence record might contain an old gene symbol, a current official gene symbol, or no gene symbol at all but just the full spelling.

Therefore, if a user wants to do a comprehensive search of the sequence databases for a gene of interest, it is often helpful to first identify the various names by which the gene has been known. The user can then construct a query that includes the various synonyms: full spelling of gene name, official gene symbol, and aliases. A good place to look for that type of information is the web site of the nomenclature committee for an organism of interest, or a curated, gene-centered database such as Entrez Gene.

1. Entrez Gene - retrieve record for human presenilin 1 gene


• do a basic search by simply entering the following query in the text box: human presenilin 1
• follow the link for PSEN1 (GeneID: 5663) to display the complete record for that locus.
• under the graphic that shows the genomic context of the PSEN1 gene, the descriptive information includes Gene name: PSEN1 and Gene aliases: AD3; FAD; PS1; S182


2. Demo: Try a few searches of Entrez CoreNucleotide database to see how the inclusion of synonyms in a search can achieve more comprehensive retrieval than searching only for the full spelling or one of the gene symbols. Enter each of the following queries as a separate search and compare the number of records retrieved:
   
   
   • human[orgn] AND PSEN1[gene]
   • human[orgn] AND presenilin 1[titl]
   • human[orgn] AND (presenilin 1[titl] OR PSEN1[gene])
   • human[orgn] AND (presenilin 1[titl] OR PSEN1[gene] OR AD3[gene] OR FAD[gene] OR PS1[gene] OR S182[gene])
   
   Note: While the alternative gene symbols noted in the last search have been applied in the past to the presenilin 1 gene, it is also possible that submitters of nucleotide sequences might have used some of those symbols to represent other genes. Therefore, the last search might also retrieve some extranneous sequence records.

There are four different ways you can search an individual Entrez database, as decribed in the module slides. The example above demonstrates a basic search.

For users who do not want comprehensive retrieval, but instead prefer a concise set of representative sequences, see the exercise on find concise summary of sequence records for gene of interest.