Gene groups help

Introduction

We strongly encourage naming families and groups of genes related by sequence and/or function using a “root” symbol. This is an efficient and informative way to name related genes, and already works well for a number of established human gene groups. Our gene groups data are now fully searchable via our search tool, please see search help for further information.

Gene groups index

Our gene groups index is ordered alphabetically according to group name, with root symbols shown in a separate column. Results are paginated and the user can choose to alter the number of results per page. Typing in either search box narrows down the results based on the input, as shown in the example below.

Gene group index
Figure 1: The gene group index.

Gene groups pages

An example gene group page for Cytochrome P450 family 4 is shown below.

Example gene group report
Figure 2: The gene group page for "Cytochrome P450 family 4"

Gene group names, IDs and aliases

Each gene group has a unique numerical ID that forms the last part of the gene group page URL to aid linking and downloading. For example the numerical ID for “Cytochrome P450 family 4” is 38. Each group also has a unique gene group name and, where a group has a root symbol, this is shown in parentheses next to the name. Please note that not all gene group pages equate to a particular set of genes with the same root symbol; in these cases only a gene group name is displayed. Other commonly-used gene group names and abbreviations are listed following the text in the “Also known as:” section.

Gene group hierarchy map

The gene groups pages provide a display of curated hierarchical relationships between groups and allow users to browse easily through each hierarchy. All gene groups that fall into hierarchies include a "Gene group hierarchy map". By default each gene group box contains a link to that particular gene group page. The rearrange mode gives a user the option to move the boxes within the graphic, e.g. for use in a screenshot. Please note that the hyperlinks will no longer work when using this function. Clicking and holding the mouse button highlights the current gene group and its direct relatives, and highlights the path between them. To return to the default mode and to re-activate the links click on the rearrange mode switch once more.

In addition to the map, text links to any related groups are provided within the page. For example, in Fig 2 there are direct links to the Cytochrome P450 family 4 subfamily A and Cytochrome P450 family 4 subfamily B .

Gene group descriptions

Many of our gene group pages contain a description of the group. These are often from Wikipedia (as shown in Fig 3) or UniProt (e.g. Cytochrome P450s), in which case the source is clearly marked with a link through to the original page. In some cases the descriptions have been written by VGNC curators and these can be identified by [Source: VGNC]; if they come from another source this will be clearly displayed within square brackets.

Example description and domain graphic from a gene group report
Figure 3: The description and domain graphic for "Cytochrome P450 family"

Example gene mapped domains graphic

Where gene group members share a particular protein domain we often show a graphical display of the protein domain structure for an example gene group member, which is sourced from Pfam via UniProt ID. In Fig. 3 the domain structure is shown for the product of the marmoset CYP1A1 gene. Hovering over a domain within the graphic will reveal a label containing the domain name, description and Pfam family ID, while clicking on a domain takes the user through to the Pfam description page for that domain.

Genes within the group

VGNC Symbol Reports for each gene within a group can be accessed by clicking on the Approved Symbol. By default the table of group members is sorted by Approved Symbol, but where the group shares a root symbol the members can be sorted by that symbol even where it is a synonym or previous symbol, the symbol used for sorting is highlighted in green to make this clear.

Gene group downloads

We now provide a way of downloading gene groups as data sets, allowing users to choose between downloading a single group or the entire group hierarchy. For example, users can choose between downloading all the Cytochrome P450 family 4 genes shown in Fig 2 or they can browse through to the Cytochrome P450 family 4 subfamily A and download just the genes belonging to that group. Each gene group page has a download link at the bottom of the page that generates a text file with all gene symbols and extra data fields such as “Approved Name” and “VGNC ID”. Please note that some gene group pages do not contain a list of genes because these are included to complete the hierarchical structure; these pages enable users to download all the genes from further down the hierarchy, e.g. Cytochrome P450s.

Summary of core data fields

Gene group name and root symbol
At the top of the gene group report page we display the group name and if applicable the common root symbol of the genes associated with the gene group within rounded brackets.
Also known as
Synonymous names for the gene group.
A subgroup of
This field contains links to groups that the current group belongs.
Group contains the following subgroups
Contains links to sub groups within the current group.
Comments
This field contains useful information about the gene group supplied by one of our curators.
Specialist advisors
Names of specialists that advise and recommend appropriate gene symbols to the committee for a particular gene group.
External resources
Links to resources that will provide extra information about the current group.
Publications
References pertinent to the gene group. The user can choose to view these references at either PubMed or European PubMed Central. This section does not aim to list all possible published papers on the group but provides links to papers that first described the gene group in question or papers that are particularly relevant to the nomenclature of the genes.
Downloads
Download gene group data in a csv text format.