How to make best use of EuroPhenome.
Quick Start Guide
A:Phenome Data Viewer
The Phenome Data Viewer allows the user to view graphical representations of the raw phenotyping data on baseline or mutant strains. The interface enables the user to select baseline strain/s or mutant/s, then choose the procedure/s and parameter/s measured they are interested in. The submission of this form, will return graphical representations of the raw phenotyping data for every parameter in each procedure. At this point the user can also download the raw data that they have choosen as well as view overview statistics of the data shown in the graps.
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 test. The significance shown is based on the probability (p) that a result that far from expected or more would be achived 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 achived under the null hypothesis that all samples came from a single normal distribution.
The levels for both tests are: Not signifigant - p > 0.05; Signifigant - p < 0.05; Highly signifigant - p < 0.001.
B:Ontology Tree back to top
The Ontology Tree viewer allows the user 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.
C:View all mutant strains
The View all mutant strains allows the user to view a table of all mutants in or finished the phenotyping pipeline from germ line transmission to phenotyping pipeline complete. The table can be ordered by column. The table links the data to further information about the clone, the gene, the allele in the EUCOMM, Ensembl and MGI databases respectively
D: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, green or grey. Red indicates a significant result at a p range of 0.0001, the green 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.
E:Information back to top
For information about EuroPhenome, help on using the tools provided then please browse the information pages listed in this panel.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 behavioral 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:Other tools back to top
Other tools available from EuroPhenome are;
Find a SOP in the EMPReSS database
View the EMPReSS Slim pipelines
Eumorphia data browser-View data from the predecessor to Europhenome
Mine Eumorphia data with biomart