The two major choices the user has in the "Europhenome Interface" interface is to view phenotype data based on a Gene of interest or a Mammalian Phenotype (MP) ontology term. You can also access phenotype data from the EMPReSSlim Pipeline for inbred mouse strains.
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 view 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.
You can view simple descriptive statistics, as well as the result of statistical significance tests between the mutant and baseline results.
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 are displayed. This information can also be viewed at the level of a whole pipeline, procedure or across all MP terms from the "heat map", or by browsing the MP tree with the "Mine for a Mutant" tool.
If you want to define a more complex phenotypic description based on a number of MP terms click 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.
Select the "Baseline Data Viewer" link from the main page. 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, and then 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.
The procedures that have been utilized to perform the test and generate the data in Europhenome are stored in EMPReSS database. You can browse them from the "Find a SOP" link.
The progress of mutant lines through the project is displayed from the "View all mutant strains" link.
The data from Eumorphia, the predecessor to Europhenome, can be viewed either by the "Eumorphia data browser".
You can search for a term, either a mutant line or in the procedure description, with the search box.
If you wish to register you get further functionality, such as saving your Complex Phenotypes and declaring interest in a certain mutant line or MP term so as to receive updates.
I hope you find this resource useful, please give us your comments at EuroPhenome HelpDesk (email@example.com).