PhenoHM

Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract PhenoHM is a human-mouse comparative phenome-genome server that facilitates cross-species identification of genes associated with orthologous phenotypes.

Combining and extrapolating the knowledge about the roles of individual gene functions in the determination of phenotype across multiple organisms improves our understanding of gene function in normal and perturbed states and offers the opportunity to complement biologically the rapidly expanding strategies in comparative genomics.

The goal of PhenoHM is to allow the user to rapidly obtain a mapping between the human and mouse phenotypes.

The tool further aids the user by providing a tree ontology view of the mouse phenotypes.

The Human Phenotype records are mapped to the mouse phenotype records based upon the common disease CUI (Concept Unique Identifier) from UMLS (Unified Medical Language System).

For this common CUI, the human genes from the human phenotype and the mouse genes from the Mouse Phenotype (MP) are fetched. Based upon these two (2) sets of genes, the ortholog genes are calculated.

The Online Mendelian Inheritance in Man (OMIM) Records and PubMed IDs from human and the MP terms and descriptions are provided in the results as evidence for the mapped human-mouse phenotypes.

By cross-mapping mouse-human phenotype terms, extracting implicated genes and extrapolating phenotype-gene associations between species, PhenoHM provides a resource that enables rapid identification of genes that trigger similar outcomes in human and mouse and facilitates identification of potentially novel disease causal genes.

PhenoHM Server Overview --

PhenoHM Server consists of four (4) sections:

1) Search Box - It lets a user enter the terms they wishes to search for.

2) Search Results - Provides a summary of the search results produced during a search query.

The first row repeats the searched term and provides the number of results searched. The second row tells where all the search term did hit a match.

The summary includes the matched Mouse Phenotype Identifier (MPID) Human Phenotype Identifier (HPID)s and their corresponding MP(HP) Terms.

3) Ontology View - Lists the Mouse (Human) Phenotype Ontology view. The root phenotype terms are colored as blue.

The root terms can be expanded to get their children and so on. After a term is searched for, the tree expands to make the matched MPID (HPID)s visible (bolded and in magenta color).

4) WorkSpace - This section is where the details of the Search results are displayed.

a) Mouse Phenotype Results - Provides a description of the mapping between the Mouse Phenotype (MP) terms and the Human Phenotype (HP) Terms.

Summary - Contains three (3) tables:

1) Mapping of Mouse Phenotype to UMLS “Disorder” Concepts;

2) Mapping of Mouse Phenotype to Human OMIM Records; and

3) Combined Results for Mapping of Mouse Phenotype to UMLS “Disorder” Concepts and OMIM Records.

The information represented in each table can be categorized into four (4) parts.

The first part represents information about the Mouse Phenotype, that is, the MPTerm, MPDescription and the total number of mouse genes associated with the MPTerm.

The second part contains the Score that has been assigned to the mapping by the SKR tool.

The third part contains information about the human phenotype, that is, the matched CUI, CUI Term, total number of human genes and the number of OMIM Records linked to the Concept Unique Identifier (CUI) Term.

The last (fourth) part contains information about the Orthologous phenotype, that is, the number of mouse specific genes, human specific genes, and orthologous genes.

Detailed Description - After clicking the ‘MPID’ at “Click Here to view the Complete Map” option a new window showing the detailed description is opened.

This page contains a detailed description of the Human-Mouse Phenotype mapping. The summary section has been provided with anchor tags to fetch detailed information about the summary terms in the ‘Detailed Description’ section.

The detailed information includes a description of Mouse Phenotype Identifier (MPID) and CUI, a description of the human, mouse and orthologous genes,(including GeneIDs, symbols, definition PubmedID and evidence code) and a description of the OMIM records associated with the human phenotype (including OMIM ids and their description).

b) Human Phenotype Results - Provides a description of the mapping between the Mouse Phenotype terms and the Human Phenotype Terms.

Summary - Contains only one (1) table:

1) Mapping of Human Phenotype to Mouse Phenotype based on Concept Unique Identifier (CUI).

The information represented in this table can be categorized into four (4) parts.

The first part represents information about the Human Phenotype (HP), that is, the HPID, HPTerm and the total number of HP genes associated with the HPTerm.

The second part contains the CUI commonly associated with the Human and Mouse phenotypes mapped.

The third part contains information about the Mouse Phenotype (MP), that is, the matched MPID, MP Term, total number of mouse genes.

The last part contains information about the Orthologous phenotype, that is, the number of mouse specific genes, human specific genes and orthologous genes.

Detailed Description - After clicking the ‘HPID’ at “Click Here to view the Complete Map” option a new window showing the detailed description is opened.

This page contains a detailed description of the Human-Mouse Phenotype mapping. The summary section has been provided with anchor tags to fetch detailed information about the summary terms in the ‘Detailed Description’ section.

The detailed information includes a description of Human Phenotype Identifier (HPID) and CUI, a description of the human, mouse and orthologous genes,(including GeneIDs, symbols, definition PubmedID and evidence code) and a description of the OMIM records associated with the human phenotype (including OMIM IDs and their description).

PhenoHM Search by MPID or HPID --

This search can be done on the basis of MPIDs or HPIDs.

PhenoHM Search by any other term --

This feature lets the user search for the MPID (HPID)s associated with the ‘any searched’ term.

PhenoHM Download Cytoscape compatible XGMML files for Mouse Phenotype (MP) to OMIM mappings --

The MP to OMIM mapping can be viewed in Cytoscape - (see G6G Abstract Number 20092) through XGMML file formats. These files are created for download by clicking the links (for each score) named “[xgmml]”.

PhenoHM Export Search Results --

The results of any search can be exported as an Excel file.

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site PhenoHM

Price Contact manufacturer.

G6G Abstract Number 20652

G6G Manufacturer Number 104252