Searching for a gene

 

Performing a simple gene search

Let's start with a simple gene search from the IMPC homepage. We will use Nbeal2 (neurobeachin-like 2) as an example.

Searching for nbeal2

Figure 6 Searching for the Nbeal2 gene.

 

Steps

Try it for yourself....

Enter the term 'Nbeal2' into the search box on the homepage (arrowed in Figure 6). As you start typing the first three letters, the search engine will make a list of relevant suggestions. This is the case for any type of search on the IMPC portal.

 

Gene summary and ordering knockout mouse strains

At the top of the results page you will find a summary box for your gene of interest, in this case Nbeal2 (Figure 7). Here you can learn more about this gene via International Mouse Informatics (IMI), Ensembl and Gene Browser links. You will also be able to quickly establish:

  • Whether there any embryonic stem (ES) cells and / or knockout mouse lines available for your gene. If knockout mice or ES cells are available, you will see a link to the repository where you can buy them directly (Figure 7A);
  • If there is any phenotypic data associated with this gene (Figure 7B).

 

Figure 7 A summary of the information available for Nbeal2.

Registering for updates

If you want to follow a particular gene, you can register your interest (Figure 7C). The IMPC will then send you an email when new data is published or a knockout line becomes available for this gene. The portal is constantly being updated as the project evolves.

 In the next few carousel pages, we will explore what phenotype data is available. 

Phenotype associations

Just beneath the gene summary you will find a phenotype summary, which provides a snapshot of the phenotypes associated with your chosen gene (Figure 8).

You will notice a selection of symbols representing the major phenotype categegories - hovering over these symbols gives you a short explanation of the phenotype (Figure 8A). Symbols are highlighed in blue when a specific phenotype has been identified. On the left hand side is a text summary which contains links to the phenotype pages as well as information on which sex(es) and zygosity the phenotype was identified in (Figure 8B).

 

Figure 8 Phenotype associations for Nbeal2.

Below the summary box is a more detailed table containing phenotype associations for your gene of interest (Figure 8C). Clicking on the graph icon (arrowed) takes you to an interactive graph that can be tailored to your needs. For example, you can visualise the data by date and also remove unwanted noise, allowing you to focus on the control or experimental data. 

Where data is available but not yet complete, a pre-QC phenotype heatmap will appear beneath the table. This analysis is likely to change as more data becomes available, so should be treated with caution.

Find out more

You can learn more about the phenotype association data by exploring the documentation section.

 

Phenotype-associated images

Where available, the IMPC portal will also show you phenotype-associated images of these knockout mouse lines (Figure 9). These images have been annotated using Mouse Anatomy (MA) and Mammalian Phenotype (MP) terms.

Figure 9 Phenotype-associated images for Nbeal2 knockout mice.

Beneath this section is a list of potential disease models and direct links to repositories where you can order ES cells and the same mice strains that were phenotyped in this project.