Genenames.org: the HGNC resources in 2013

Abstract

The HUGO Gene Nomenclature Committee situated at the European Bioinformatics Institute assigns unique symbols and names to human genes. Since 2011, the data within our database has expanded largely owing to an increase in naming pseudogenes and non-coding RNA genes, and we now have >33,500 approved symbols. Our gene families and groups have also increased to nearly 500, with ∼45% of our gene entries associated to at least one family or group. We have also redesigned the HUGO Gene Nomenclature Committee website http://www.genenames.org creating a constant look and feel across the site and improving usability and readability for our users. The site provides a public access portal to our database with no restrictions imposed on access or the use of the data. Within this article, we review our online resources and data with particular emphasis on the updates to our website.

Figure 1.

The statistics and downloads page allows users to retrieve plain text, tab-separated data sets. The user may download the entire gene symbol report data set, gene family sets or download data that belong to a certain locus type. The table on the page shows the total number of entries per locus group and type including all of the non-coding RNA locus types and the number of entries associated to them.

Figure 2.

A typical gene symbol report showing the shaded box containing the HGNC core data with other information and links below. If the gene is within a gene family, then the gene family field will also be displayed. The new banner featuring a new logo and colour scheme is at the top of the image. The banner contains a simple quick search box to the right and holds tabs that produce drop-down menus, once the mouse cursor hovers over the tab. The website footer containing our affiliations, funding sources and policies is seen at the bottom of the page. The footer also sports an email link so that users can contact us via the link.

Figure 3.

An example of an information dialog pop up that appears if the keys ‘C’, ‘D’ or the dagger symbol are selected. When the dialog box appears, the background is greyed out, and the dialog comes into focus. The dialog box is scrollable if the text within does not fit into the 400 by 300 px box.

Figure 4.

The most common way of browsing for gene families is shown in the figure. The flow through the pages is seen by following the arrows from image a to image d. From the header, a user would select an option from the drop-down shown (a). This then takes the user to a families list page (b) in which the user selects a family, bringing them to the family page (c). From the family page, the user may then select a gene symbol, taking them to a gene symbol report (see Figure 2).