Search Genes Documentation
Search Genes Tools Overview
genenames.org provides three distinct tools for searching the HGNC approved nomenclature:
This search is also available on the homepage. The tool allows fast, simple searching of HGNC data and is perfect for those who want to check a gene symbol against our database, or who want to locate the Gene Symbol Report for a particular gene using the gene symbol, a database ID or a synonym.
This allows you to build a more specific query than Quick Gene Search. You can choose to search within specific datasets e.g. only for approved symbols. There are four available query segments that you can use to build your search. These segments can be combined using the functions 'AND' and 'OR'.
This search allows you to search for multiple genes by gene symbol in one rapid step. Use List Search when you want to check the nomenclature of many symbols at once e.g. you are about to submit a paper and want to check that the gene symbols you have included match approved nomenclature.
Here is a full guide to using each of the three tools:
Enter any of the following types of search term in the Search Genes box:
- gene symbols
- gene names
- keywords e.g. part of a gene name
- IDs - Quick Gene Search supports queries using HGNC database IDs and IDs from the following external databases: Ensembl, Entrez Gene, Vega, MGI(mouse gene ortholog IDs), RGD (rat gene ortholog IDs), CCDS (consensus CDS IDs), Enzyme Commission, pseudogene.org
It is possible to enter multiple search terms e.g. three gene symbols; two database IDs; a combination of keywords. Search terms can be separated by commas or simply by spaces.
Decide whether your results should equal, begin or contain your search term by checking the radio buttons.
Step 3 (optional)
Quick Gene Search shows 50 hits per results page by default. You can use the dropdown menu to change this to a different number of hits per page, or to display all hits on one results page.
Click the magnifying glass icon to submit the search.
Review your results.
The results table displays the approved symbol, gene name, and chromosomal location. There is also a "best match" column that shows why each result has been returned by displaying the HGNC data field that best matches the search term i.e. Approved Gene Symbol, Approved Gene Name, Synonym etc. The matched data is indicated in this field by red highlighting. To view more information on a result, click on the approved symbol to be taken to the Symbol Report for that particular gene.
Quick Gene Search ranks your results in order of relevance. For example, searching records that contain 'TP53' will return the approved gene symbol TP53 at the top of the results list; gene symbols that contain TP53 such as TP53AIP1 rank lower down the list; genes with a previous symbol containing TP53 rank lower still (e.g. the TP53AIP1 is a previous symbol of ANO9); genes with a synonym containing TP53 rank lower; genes with TP53 in the name are further down the results list. If you have searched for two keywords, Quick Gene Search will return results that pertain to both keywords at the top of the results list, and will display results that relate to only one or other of the search terms further down the results list.
The Advanced Gene Search allows you to build a complex query using different query segments. Each query segment allows you to specify the type of data that you want to search for.
Select the type of data that you would like to search for from the dropdown menu for your first query segment. Each query segment has the following options:
All Records - searches through the same data fields as described for the Quick Gene Search above (gene symbols, names, synonyms, keywords, database IDs)
Approved Symbols - searches only within the approved symbol data field
Approved Gene Names - searches only within the approved name data field
HGNC ID - searches only for HGNC IDs
All Symbols & Synonyms - searches within the approved symbol, previous symbol and synonyms data fields.
Chromosomes - searches within the chromosomal location field
Previous Gene Names - searches for previous approved gene names. Please note that this is for previous full gene names only; choose All Symbols & Synonyms to search for previous symbols
Any ID number - allows searches with the following database IDs: HGNC, Ensembl, Entrez Gene, Vega, MGI (mouse gene ortholog IDs), RGD (rat gene ortholog IDs), CCDS (consensus CDS IDs), Enzyme Commission, pseudogene.org
Synonyms - searches for all symbol and gene name synonyms
Decide whether your results should begin with, contain or equal your search term. Advanced Gene Search also supports negative searching; you can change the second dropdown menu of the query segment to "do not" so you are searching for results that do NOT begin, contain or equal your search term.
Enter your search term in the query segment box.
If one query segment is enough to perform your search, you would hit submit at this stage. However, if you want to build a more complex query, you would repeat steps 1-3 for the second query segment. You would also need to decide how to combine the query segments for your search; the options are "AND" and "OR". Four query segments are available in total.
By default, the Advanced Gene Search shows 50 hits per results page and orders results by symbol. You can use the dropdown menu underneath the query segments to change the number of results shown per page or to order the results by chromosome instead of by symbol.
Review your results. For each result, the approved symbol, gene name and chromosomal location is shown. To view more information on a result, click on the approved symbol to be taken to the Symbol Report for that particular gene.
1. Find all genes with a gene symbol that begins with PCDH and that are on 5q.
Set the first query segment to "Approved Symbols that do begin with PCDH". Make sure AND is selected at the end of this segment.
Set the second query segment to "Chromosomes that do contain 5q".
2. Find all genes that contain either "transcription" or "activator" in the approved gene name.
Set the first query segment to "Approved gene names that do contain transcription". Select "OR" at the end of the segment.
Set the second query segment to "Approved gene names that do contain activator".
3. Find all genes with a gene symbol that begins with ABC but that do not contain pseudogene in the gene name.
Set the first query segment to "Approved Symbols that do begin with ABC". Make sure AND is selected at the end of this segment.
Set the second query segment to "Approved gene names that do not contain pseudogene".
Please note that the List Search can only be used for searching lists of gene symbols, not gene names.
Type, paste or upload a list of symbols to be searched. Symbols can be separated by commas or new lines.
Choose your search parameters using the dropdown menus under the search box. There are four parameters:
- case sensitivity - the default option is case insensitive but you can change this to perform a case sensitive search.
- data output format - the default option is an HTML table; this provides hyperlinks to HGNC gene Symbol Reports. You can choose to return data as a tab delimited text file, which can be saved and imported into tables and spreadsheets.
- inclusion/exclusion of failed matches - the default option "retaining failed matches" includes search terms that do not match any HGNC approved symbol, synonym or previous symbol in the results and indicates that these have no match. Changing the parameter to "excluding failed matches" will mean that these search terms are not included in the results at all.
- order of results - the default returns the results in the same order as the input list. You can change this to sort the results by alphabetical gene symbol order.
Click on the submit button.
Review your results.
If a particular input search term matches more than one gene record, these matches will appear in sequential rows in the results table. For example ACS3 will have two results as it is a previous symbol of TWIST1, and an synonym of ACSL3.
The results table includes the Input search term, the Match Type, the Approved Name, HGNC ID and chromosomal Location.
The Match Type column describes the relationship between each input search term and the matching HGNC approved symbol. There are 5 match types:
- matches - the input is the same as an approved symbol (note this search is case insensitive).
- synonym of - the input has been added by an HGNC editor as a synonym of the approved symbol.
- previous symbol of - the input was previously an approved gene symbol, but the gene has since been updated with the approved symbol shown.
- matches withdrawn entry - the input was an approved symbol for a gene that has since been withdrawn.
- no match - the input does not match or map to any HGNC approved gene symbol. Note that there must be an exact character match between the input and matched term. For example, OCT7 will match as a synonym of POU3F2 but OCT-7 will not.
To view more information on a result, click on the approved symbol to be taken to the Symbol Report for that particular gene. Please note this is only possible if the results are returned in the HTML table format.