Getting Started with Gene Pages

Our gene and phenotype search engine is featured throughout our website. From this starting point, you can search for more information on a gene or phenotype of interest by clicking on the relevant tab.

Choosing a gene of interest from our search engine will take you to a gene page. Our gene pages offer different types of data depending on the phenotyping pipeline used and how much of the phenotyping process has been performed.

The Gene Page

At the top of each gene page, you will find helpful information such as basic gene information, the significance per physiological system and links to sections further down the page. The basic gene information links to pages for viability phenotyping, our embryo viewer and other partner site pages for the same gene. You can hover over the icons in our significance section for more detail. If you would like updates on this gene, you can sign up with the IMPC and click the follow gene button – we will only send you emails when we update this specific gene page.

Below the top section is the phenotype section. This section is made of three tabs:

The significant phenotypes tab

This tab lists all of the significant phenotypes found by the IMPC for the gene of interest. You can use the search function to look for a specific phenotype here or download the data as a .TSV or .XLS file at the bottom of the table. You can click on any row of the table for more data on the phenotype via our data chart pages. For some phenotypes, this will just be observation rates, whilst others will have more in-depth analysis pages. These data chart pages can have details on the procedures performed, the outcome of the procedures as well as charts and statistics information. You can also access the raw data here in different file formats.

The measurements chart tab

This displays each individual procedure performed and the parameters that were measured for the gene of interest. We recommend not looking at all of the procedures that were performed at the same time as there may be too much data for the chart to function adequately. You can click and drag on the chart to zoom in on sections (use the reset zoom button in the top right corner to reset) or use the ‘deselect all’ button at the top of the chart before choosing your procedure of interest below. Selecting a procedure to view will display all the parameters for that specific test and the p-value (-Log10). The IMPC uses a significance threshold of (NUMBER), which is only displayed on the chart if a parameter crosses the threshold. You can also view procedures by physiological system using the drop-down at the very top of the tab. Clicking on any data point on the chart will take you to a corresponding data chart page.

The all data table tab

This tab shows the same information as the measurements chart in table format. Every procedure performed in listed here, which you can filter by life stage (pipeline) and by physiological system. As with both earlier tabs, clicking on a row will take you to a data chart page with more information.

EXPRESSION Section

Most gene pages have expression data sections. This section has two tabs: adult expression and embryo expression. Gene pages will have data here depending on viability test results. You can click on the question mark for more information on how the IMPC produces lacZ expression data.

If a tab has available expression data it will display a table with information on the different tissue types and expression rates. At the top of the table is a key to illustrate expression. Tissues in which the gene of interest is expressed are labelled with an orange circle with brackets containing the number of mice found to be expressing the gene. If lacZ imaging has been performed for specific tissues there will be links in the ‘images’ column. Clicking on these links will take you to our image comparator page where you can visually compare wild-type and mutant lacZ images.

All annotated lacZ images can also be viewed by clicking the images tab in the top right corner. This tab groups images by physiological group, therefore the image comparator pages linked here will give you a broader range of images than the tissue-specific links on the table tab.

ASSOCIATED IMAGES Section

The associated images section will link to all available images for the gene of interest. All lacZ images will also be linked here, as well as other image groups. The type of image group listed can vary widely and can include lacZ, X-ray imagery in various orientations, eye morphology, embryo morphology, gross pathology and tissue collection and histopathology. Clicking on the help icon in the top right corner will take you to the images help & documentation page which will explain how to find images using queries to the SOLR core.

DISEASE MODELS Section

The disease models section has two tabs. The first tab lists all disease associations by annotation and orthology and the second tab lists associations by phenotypic similarity. If associations have been made for the gene of interest then a table will be displayed. You can search for specific diseases via the search function in the top right corner. The table will tell you what database source was used for the association as well as detail for the phenodigm score. Clicking the orange help button in the top right of this section will take you to a help and documentation page which will detail more on how phenodigm scores are calculated. You can click on a row (or the black plus icon at the end of a row) for more information on each disease association.

Clicking on a row creates a drop-down. This drop-down lists the mouse models and corresponding genotypes that the disease of interest has been associated with, as well as phenodigm scores per model. The genotype column describes both the allelic composition and the genetic background of the mouse model.

At the bottom of the table is a ‘phenogrid’ displaying the phenotypes associated with the disease of interest. You can click on the small black information button above the listed phenotypes for notes on how the phenogrid layout works. Hovering over a mouse model (x-axis) will tell you more information on the model and hovering over a phenotype name (y-axis) will tell you more information about the phenotype (you can expand the classification hierarchy here too.) The phenotype squares are colour coded for similarity and the key is displayed below the grid. You can hover over a phenotype square for information of the parameters that were measured for that phenotype. All links displayed when hovering over different aspects of the graph will take you to Monarch Initiative pages displaying more information on the phenotype or parameter.

By using the phenogrid options panel, you can sort by different factors and change the calculation method. The black information icons on the options panel will tell you more information on how to use the phenogrid and you can also download the phenogrid as a .SVG file here. Below the phenogrid is a list of unmatched phenotypes with links to phenotype details on the Monarch Initiative site.

HISTOPATHOLOGY Section

Some gene pages will have a histopathology section. In this section you can find a list of phenotypes that have histopathology data. Clicking on a row will take you to a histopathology data page. This page list all of the mice that have undergone histopathology procedures. For annotated mice, this page will provide information such as severity score and significance score, both of which are explained at the top of the page. This is also accompanied by images and a description of the tissue abnormality observed. At the bottom of the histopathology page you can find all associated histopathology images for the gene of interest, which are also displayed under the ASSOCIATED IMAGES section. [NO SPECIFIC HELP PAGE LINKED TO HELP BUTTON]

ORDER MOUSE AND ES CELLS Section

You can find information and links on available products per allele here. Clicking on the orange plus sign for an allele on interest opens a drop-down. The top of the drop-down displays an image showing the allele and its mutations. Alleles will have different products available, including mice, ES cells, targeting vectors and tissues, all of which are displayed as tabs under the image.

On the ‘mice’ tab, you can find available colonies, QC data and an order/contact link. Similarly, on the ‘ES cells’ tab, you can find available ES cell clones, their QC data and order links. The ‘targeting vectors’ tab also has order links as well as a Genbank file and vector map. Lastly, the ‘tissue’ tab has email links for fixed tissue and paraffin-embedded section enquiries. [Check if these are the only two tissue types offered]

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