How to use tissue—phenotype associations provided in PhenoDigm
Browse data by phenotype
All the tissues that have been associated with a particular phenotype can be accessed through the phenotype itself. Each phenotype that is associated with at least one tissue is listed. The list can be either browsed manually and the phenotype of interest accessed with the MP term ID given in the first column, or by typing the phenotype in the search box.
Information particular to phenotype
The detailed information page for each of the phenotypes provides in addition to phenotype name and ID, the anatomical component that has been assigned in entity-quality statements.
P-values for tissue—phenotype associations have been calculated with two independent methods: a hypergeometric distribution and association rules. The p-value is provided in the detailed phenotype page if the association is deemed significant. “-” means that either no p-value could be calculated or is not smaller than 0.05. If a phenotype is associated with a tissue, the supporting genes are provided that support this association.
The data can be accessed from the FTP link on Tissue phenotype associations tab on the main page. The download file is tab delimited and contains seven columns:
- MP identifier - The Mammalian Phenotype ontology identifier of the phenotype
- MP term - The name used in the Mammalian Phenotype Ontology for the phenotype
- MA identifier - One of the 21 investigated adult tissues represented with Mouse Anatomy ontology identifier
- MA term - The name of the tissue as used in the Mouse Anatomy ontology
- pValue hypergeometric distribution - The p-value determined when applying a hypergeometric distribution
- pValue association rules - The p-value when applying the association rule mining software
- Supporting mouse genes - A ', ' delimited list of the genes (MGI gene id) supporting the p-value
A p-value of 1 in either of the two p-value columns indicates that no significant association could be established between tissue and phenotype.