The Gene page contain several subsections which will be described here.

Gene Summary

The first section of the page shows summary information about the gene. The information displayed includes:

Phenotype associations

This section shows the association of genes to Mammalian phenotype terms.

It contains 4 ways of data viewing:

(1) See all adult phenotypes
(2) See all embryo images, when available
(3) A quick glance of how phenotypes were discovered by icons
(4) Table view of significant phenotypes

(1) See all adult phenotypes:

Press the "All Adult Data" button.

You will be taken to a separate page for details of the statistical analysis. Significant P values appear to the right of the green dashed vertical line; insignificant values to the left. Hovering over any point shows some important experiment details. Clicking on any point shows a graph of the experiment data.

(2) See all embryo images:

Press the "3D Imaging" button.

You will be taken to a new page with an interactive graphical interface with which you could view the embryos




(3) A quick glance of how phenotypes were discovered by icons:

The icons on the right hand side show a visual summary of the same data. The colors indicate how significant phenotypes were discovered.

(4) Table view of significant phenotypes

This phenotype table lists the individual phenotypes associated to this gene through a specific allele. If both sexes are associated, then both are shown on the same row indicated by the male / female icons ().

The results shown in the phenotype table may be filtered using the dropdown filters. Select the check boxes to include entries pertaining to the selection. The displayed rows are the result of logically ORing within and logically ANDing between dropdowns.

Filter be top level MP term

Gene-phenotype association download

The results in the table may be downloaded for further processing. The resulting download respects all filters that have been applied to the data.

We offer 2 export options for the data in the table:

In the table displayed on our page entry lines are collapsed based on sex. That is, if for 2 lines all fields are identical except the gender, they will be shown together for a better user experience. In the export file however we export all lines separately, to allow easier further processing of the data. This holds for both XLS and TSV files.

Phenotype Heatmap

When there is data available, but not yet complete, from the IMPC resource, the Pre-QC panel will appear. The pre QC panel shows a heatmap of the results of preliminary analysis on data that has been collected by the IMPC production centers to date, but is not yet complete. In order to be marked Complete, 7 males and 7 females must complete all core screens required by the IMPC pipeline.

Please visit the comprehensive heatmap documentation for more information about the heatmap.

Please visit the IMPReSS website for more information about the IMPC pipeline.

NOTE: Use this analysis with caution as the analysis is likely to change when more data becomes available.

Below is an example of a typical IMPC heatmap.


Expression

This section displays IMPC lacZ expression data (A). In some cases where legacy lacZ expression data is available (B), they will be shown as well.


(1) IMPC lacZ Expression Data:

Eventually, all genes should have both embryo and young adult (weeks 9-16) expression data. They are organized in tabs.

(2) Legacy lacZ Expression Data:

The data are organized by anatomy terms from the Mouse adult gross anatomy ontology.

Phenotype Associated Images

A number of assays generate image data and are used by the phenotyping centers to score the presence or absence of an abnormal phenotype. Uploaded phenotype images are presented here organised by the procedure generating the image. In addition to the IMPC images, some genes have legacy ones.

The screenshot below shows the number of images grouped by procedures. Click to reveal the content.

Disease Models

Model organisms represent a valuable resource for the characterization as well as identification of disease-gene associations, especially where the molecular basis is unknown and there is no clue to the candidate gene’s function, pathway involvement or expression pattern.

Shown here are human diseases found by PhenoDigm analysis (PHENOtype comparisons for DIsease and Gene Models) which uses a semantic approach to map between clinical features observed in humans and mouse phenotype (either from MGI or IMPC phenotype evidences) annotations.

The human disease model associations are based on gene orthology or phenotypic similarity that you can browse by clicking on the respective tabs.

In the table, each row is a human disease to mouse phenotype association. To see what mouse genes (alleles) are annotated to these mapped mouse phenotypes, clicked on the "plus" icon.

Order Mouse and ES Cells

The alleles and ES cells section describes the mutations available from the IKMC resource. Each row corresponds to an allele of this gene. A diagram is included depicting the mutation the allele carries.

The links in the Order/Contact column will take you to the purchase place of the ES cell or mouse when available.

The genbank file link points to a genbank file describing the genomic sequence of the allele.