How to make best use of EuroPhenome.

Quick Start Guide

Gene Search Phenotype Search Baseline Search Mouse Strains Phenomap Empress Ontology Tree

A:Find Gene

Start typing the gene name into the "Find Gene" box on the home page. This will return a list of genes that match your search.

Select the gene you are interested in and a summary of the data we have for that gene is displayed, as well as links to other related resources. To veiw the phenotyping data click on a procedure name (select a different pipeline by clicking on its name).

You can access the phenotyping data with finer control by clicking on "Advanced Search Options". This shows you a graphical representation of the data you have requested in comparison to the inbred strain data relevant to that mutant.

Overview Statistics

The overview statistics for mutant data show the user the mean, SD, SE, significance result from a rank sum and T-test.

Rank Sum Test

This test is performed using the Mann-Whitney U test. The significance shown is based on the probability (p) that a result that far from expected or more would be achieved under the null hypothesis that all samples came from a single distribution.

T-test

This test is performed using the 2 tailed, 2 sample unpaired Student's T-test. The significance shown is based on the probability (p) that a result that far from expected or more would be achieved under the null hypothesis that all samples came from a single normal distribution.

The levels for both tests are: Not significant - p > 0.05; Significant - p < 0.05; Highly significant - p < 0.001.

B:Find MP Term

Start typing the phenotype into the "Find MP Term" box on the home page. This will return a list of MP terms that match your search that have annotations within EuroPhenome. Select the term you are interested in and a summary of the lines that are annotated to that term, as well as the parameters that generated those annotations will be displayed.

A more complex phenotypic description based on a number of MP terms is available by clicking on the "Advanced Search Options" of the phenotype search box. If you select multiple MP terms by typing them into the "Select a phenotypic term" box these terms are added to a single "Complex Phenotype". As they are added the lines that are annotated to all these terms are displayed below (lines that match some of the terms are available by clicking on the "Partial Matches" tab). You can select whether to include (default) or exclude lines that match by clicking on the "logic" condition (AND or NOT). To further refine your search click on "More Options" and you can the select the p value and effect size range you wish to consider.

C:Baseline Data Viewer

The Baseline Data Viewer allows the user to view graphical representations of the raw phenotyping data on baseline strains. You can then select the phenotyping test of interest. To further refine your query select advanced search. This will then give you a number of choices to select: the relevant inbred strains, the centres that performed the procedure, the procedure of interest, the parameters. Submit the request by clicking on "Update" to return a graphical display. You can also view simple descriptive statistics for the strain(s) of choice.

Overview Statistics

The overview statistics for baseline data, show the user the mean, SD and SE.

D:View all mutant strains

The View all mutant strains viewer allows the user to see a table of all mutants for which we have data. The table links the data to further information about the clone, the gene, the allele in the EUCOMM, Ensembl and MGI databases respectively as well as to the EuroPHenome summaries for that line.

E:View PhenoMap back to top

The The PhenoMap is a visual 'heatmap' representation of all the significant phenodeviants and their ontology annotations. The map shows the mutant strains along the vertical axis and the procedures across the horizontal. Each box is coloured red, blue or grey. Red indicates a significant result at a p range of 0.0001, the blue indicates no significant result and grey means it wasn't tested. The Phenomap is interactive and allows users to choose the pipeline of interest, and the P range and /or Effect Size they believe is important for the phenodeviant they are searching for. You can also view this data arranged by ontology term with the Beta Ontology Heatmap.

F:EMPReSS back to top

EMPReSS provides a comprehensive database of validated Standard Operating Procedures (SOPs) for screens to determine the phenotype of a mouse.

EMPReSS incorporates more than 150 new SOPs. These cover all of the main body systems including; clinical chemistry, hormonal and metabolic systems, cardiovascular, allergy and infection, renal function, sensory function, neurological and behavioural function, cancer, bone and cartilage, and respiratory function.

In addition, there are generic SOPs in histology, necropsy, pathology and gene expression.

The procedures utilised in the EMPReSSlim pipeline are available in EMPReSS.

G:Ontology Tree back to top

The Ontology Tree viewer allows the user to browse the MP (Mammalian Phenotype) ontology tree, to view phenodeviants annotated with specific phenotype ontology terms. For further information on the annotation pipeline please read the FAQ.

Other tools back to top

Other tools available from EuroPhenome are;

For further help you can visit the Quick Start Guide