Our phenotype page consists of three main parts: the phenotype information/details, the gene associations summary and the table of gene variants associated with the current phenotype.

Phenotype Summary

The synonyms and definitions we provide come from the mouse phenotype ontology (MP), which is administered by Mouse Genome Informatics (MGI). Use the provided MGI link to go to the MGI MP browser.

The procedures come from IMPC pipelines and from legacy data pipelines such as EUMODIC and GMC.

Phenotype Association Stats

IMPC mouse strains are subjected to a wide range of phenotype assays, allowing for estimates on the percentage of genes that, when knocked out, contribute to a phenotype. As multiple parameters may map to the same phenotype, percentages are calculated across all parameters that map to a phenotype.

The percentage of genes associated to the current phenotype in one sex only (for example, females) is the number of genes associated to phenotype X in females divided by the total number of genes tested in females for parameters potentially leading to phenotype X associations. Thus, the percent values we show for females and males may not add up to 1, nor do the percentages for males/females have to be smaller than the combined percentage.

We consider "tested" for a phenotype a gene for which at least one parameter potentially leading to this phenotype association has data and has been statistically analyzed by our pipeline.

Currently the data used for this panel is restricted to IMPC data on B6N strains. Mutant strains with the phenotype associations appear in the gene-phenoytype table found further down the phenotype page.

Overview Graphs

As the data is extremely varied, for instance, in what controls are selected, what is represented (e.g. individual animals vs strains), and the nature of the values (e.g. means, count, etc.), each is described separately below.

Chart Filters and Selectors

Multiple parameters can indicate the same phenotype. When this is the case, a drop-down list will appear on top of the list allowing you to select the desired parameter.

The filters under the chart allow you to filter the plotted data based on sex and phenotyping center.

Unidimensional Data

Unidimensional data is plotted as stacked histograms. We take the mean for each line and plot these values as a histogram. Mutant lines that have been associated to the phenotype are highlighted, including those lines where the phenotype was only observed in one gender or zygotic state. Some lines may be associated to a phenotype but may not appear to be an outlier. This usually results from controls having relatively low or high values in the time period the mutant lines were tested.

[Tip] The bars are clickable and will take you to a multi-chart page to analyze the data more closely.

Categorical Data

Categorical overview charts represent the percentage of strains in each category. These graphs only display for categorical parameters at the line level (as opposed to animal level), such as fertility or viability parameters. The animal-level parameters can only be analyzed in the individual charts linked from the associations table.

Gene-Phenotype Associations

All gene variants associated with the current phenotype are shown in a table. The table contains several fields of interest, such as the gene name and the corresponding allele, zygosity, sex, data source, parameter, a link to the chart when one is available, as well as the procedure used, and directly associated phenotype. The directly associated phenotype is particularly useful for higher level phenotype terms. See Direct vs. inferred associations for more information.

Row Collapsing

For better readability, when rows are identical in all fields except for sex, they are collapsed into a single row. Such rows are identified by a both-sexes icon (). Regardless of row collapsing, the total number of results shown at the top of the table includes all males and all females.

Direct vs. inferred associations

Some associations are direct calls from our statistical pipeline, whereas some are transitively associated, infered from the direct lower level associations. The value in the 'Phenotype' column will help you disambiguate at which level the gene-phenotype association was made.

Pre-QC vs. Post-QC Calls

Preliminary statistical analysis is performed at the DCC as soon as enough data is gathered, prior to rigorous quality control checking. This analysis produces results, but due to the preliminary state of the QC checks, the results are considered not definitive. Once the data has passed the QC checks at the DCC, a final definitive statistical test is performed and the MP association is made.

Post QC calls are presented in the associations table and have blue chart links.

Pre-QC calls are presented in the associations table and have orange chart links in that table and in the heatmap below the table.

Table Filtering

The filters over the gene variants associations table offer flexible filtering possibilities. Multiple checkboxes can be selected from any filter dropdown list and the table will automatically reload with each new selected option. These changes will be mirrored by the total number of results over the table as well as by the table export.

Multiple filters from the same dropdown list are joined by a logical OR. Filters between different lists are joined by a logical AND.

Downloading Results

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 two export options for the data in the table: text file with tab separated variables (TSV) and Microsoft Excel spread sheet (XLS)

Please note: while collapsed rows are shown on the page, download file rows are not collapsed; the download file contains a single row for every mouse.