This help document answers the following questions:
Use this query form to find phenotype and disease associations for human and mouse genes and genome regions. You can enter a combination of multiple phenotype terms, disease terms, gene symbols, accession identifiers (IDs) and genome coordinates.Top
|phenotype||A description of the observable state of an individual with respect to some inherited characteristic. See also dominant and recessive in the MGI Glossary.|
|disease||A human disease, syndrome, or condition listed in the OMIM (Online Mendelian Inheritance in Man) database.|
|allele||One of the variant forms of a gene, differing from other forms in its nucleotide sequence. Allele category, allele combination and allele pair also appear in the MGI Glossary.|
|allele name||In MGI, an allele name is a word or phrase that uniquely identifies an allele of a given gene. The allele name has an abbreviation that is the allele symbol added as a superscript to the gene symbol. See also Gene Name in the MGI Glossary.|
|allele symbol||In MGI, an allele symbol is a unique abbreviation for the allele name of a given gene. Allele symbols take the form of superscripts added to the gene symbol. See also Gene Name and Gene Symbol in the MGI Glossary.|
|See Allele Combination in the MGI Glossary.|
Note: Some terms may have unique definitions in the context of MGI queries and results. For more information, see:
|Search by Genes | Genome Locations | Disease or Phenotype Terms|
|Search by genes||
Symbol, name, synonym, homolog or ID for a human or mouse genetic marker.
|Search by genome locations||You can enter a list of mouse or human genomic regions (e.g. 2:105668896-108698410, 13:22210730-22311689) and use the radio button to specify the species (Mouse or Human). You can enter multiple regions separated by commas, spaces and/or returns. Use MT for the mouse mitochondrial chromosome.
|Search by disease or phenotype terms||The Search by disease
or phenotype terms section is a full-text search field.
Yes. The mammalian phenotype terms are from the Mammalian Phenotype (MP) Ontology, a community effort to provide standard terms for annotating phenotypic data. The Mammalian Phenotype Ontology has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. You can either browse or search the Ontology with the Mammalian Phenotype Browser. You can use this browser to view terms, definitions, and term relationships in a hierarchical display. Links to summary annotated phenotype data at MGI are provided in Term Detail reports. See Using the Mammalian Phenotype (MP) Browser for additional help.Top
Yes. The disease vocabulary contains human disease, syndrome, and condition terms from Online Mendelian Inheritance in Man (OMIM). You can browse the vocabulary and find links to full OMIM records and mouse model information by using the Human Disease Vocabulary Browser. Navigate the vocabulary until you find the term you are looking for. See Using the Human Disease Vocabulary Browser for additional help.Top
Yes, you can use the disease or phenotype terms box to search for phenotypes OR diseases.Top
Yes, you can.
Use the radio buttons to specify the species and click Choose File to browse for your VCF (Variant Call Format) file.Top
An error message is generated if:
The form has been tested only with VCF v4.0 and higher standard formats.Top Top
The Gene Homologs x Phenotypes/Diseases tab, the default selection, provides an overview of your results in a grid format. The query summary contains the following fields:
Human Gene Symbol of the gene, linked to homology information. Mouse Gene Symbol of the gene, linked to its MGI gene detail record. Phenotypes And Diseases Starting from the left are high level terms from the Mammalian Phenotype (MP) Ontology annotated to alleles of the mouse gene. See also the Mammalian Phenotype Browser. Phenotypes that are only annotated to complex genotypes—those involving more than one genome feature—are not listed in this summary. Phenotypes to all the genotypes associated with an allele can be viewed by following allele symbol links to Allele Detail pages. Listed to the right, after a vertical grey bar, are human diseases associated with the human gene in OMIM or through mouse models described in publications.
Currently only mouse phenotypes are returned. Human phenotype data will be available in a future release.
Some of the human disease terms have been shortened and end with an elipsis. If you hover your cursor over the term, a pop-up will display the full term name. Highlighted column titles indicate which columns contain phenotype or disease terms that match one or more terms in the search. Highlighting is only displayed on column titles, and only when a phenotype or disease term is used in the search. A column is highlighted when at least one of the genes has an annotation matching your search. So if you search for a general term such as fibrosis, the cardiovascular system column may be highlighted because one gene is associated with cardiac fibrosis. Another gene may not have cardiac fibrosis but is returned because it is associated with pulmonary fibrosis, causing the respiratory system column to be highlighted. Columns that are not highlighted contain additional phenotypes and/or disease terms associated with the mouse model or human gene that is connected to the searched term(s).
The colors, blue for mouse data and tan for human data, get progressively darker with more supporting annotations. The lightest color represents one annotation. 2-5 annotations is represented by a darker shade, 6-99 annotations darker still and more than 100 annotations by the darkest color.
You can hover your cursor over a colored square to see that row's markers and column heading in a pop-up.
Click on a colored square for information on mouse genotypes and lower level phenotype terms. The mouse genotypes link to even more detailed phenotype information.
A bold N in a phenotype column indicates that no abnormal phenotypes of that type were observed in any allele of the gene.
You can filter the grid to show only specified columns and rows by checking the appropriate boxes and clicking the Apply Filters button or the filter icon.
If you select the Genes tab, the query summary contains the following fields:
Organism States whether the corresponding marker is human or mouse Gene Symbol Symbol of the gene. Mouse genes are linked to their MGI gene detail records. Human genes are linked to their Vertebrate Homology Class pages. Vertebrate Homology Class pages provide links to Entrez Gene and the ability to download sequences in FASTA format for several vertebrate species. Genetic Location The chromosome and genetic map position for the marker are shown if known. Genome Coordinates The marker's chromosome basepair coordinates, strand and genome build are shown if known. Associated Human Diseases Lists any human diseases described in Online Mendelian Inheritance In Man (OMIM) that are associated with the marker. Disease associations for human markers are from the NCBI mim2gene_medgen file and include annotations from OMIM, NCBI curation, Gene Reviews, and Gene Tests. Mouse markers are associated with human diseases through genotypes described in publications. Abnormal Mouse Phenotypes Reported in these Systems High level terms from the Mammalian Phenotype (MP) Ontology annotated to alleles of the mouse gene. See also the Mammalian Phenotype Browser. Phenotypes that are only annotated to complex genotypes—those involving more than one genome feature—are not listed in this summary but can be found in the Phenotypic Allele Detail Report. References For mouse markers, a link to all the references for the marker is provided. A separate link may be present that links to the just the disease relevant references. The reference summary provides the abstract and links to MGI curated data and when possible, links to PubMed and Journals. Mice With Mutations In this Gene (IMSR) Shows the number of stocks in the International Mouse Strain Resource (IMSR) that contain an allele of the gene. The number links to the IMSR which provides access to stock repositories.
The default sort for this tab is by Marker Symbol, though you can choose to sort by Organism or Genome Coordinates by clicking the column headings or the up/down arrowheads ( ▼ ▲).
If you select the Diseases tab, the query summary contains the following fields:
Disease The OMIM disease term linked to the MGI Human Disease and Mouse Model Detail page OMIM ID The Online Mendelian Inheritance In Man (OMIM) accession ID Mouse Models The number of mouse models for this disease Associated Genes from Mouse Models The mouse markers used to create the various models of this disease Associated Human Genes Human genes associated with the disease. Disease associations for human genes are from the NCBI mim2gene_medgen file and include annotations from OMIM, NCBI curation, Gene Reviews, and Gene Tests. References using Mouse Models The number of references describing mouse models of the disease, linked to reference details and curated data
You can filter by Genome Feature Type. In your results, click Filter results by: Genome Feature Type and check the desired types. This will reduce your results to only those containing the checked items. The filters are applied across all data tabs and to any file you export.Top
Yes. The Genes and Diseases tabs but not the Gene Homologs x Phenotypes/Diseases tab, provide a tab-delimited text export option. In your search results, click on the Text File icon. Your web browser will download a file of the results.Top
Paste your list as a column or separated by commas or spaces into the Search by genes field. For example: APP, PLAU, PSEN1, CAV1, NOS3, 10513
Click the GO button.
The search finds matching mouse and human genes and synonyms, and their homologs and associated mouse transgenes, and displays phenotypes associated with allele pairs of the mouse genes and transgenes, and diseases associated with both the human and mouse markers.
Paste your genomic coordinates for human build GRCh38 in the center, Search by genome locations, section of the form:
chr22:18217079Check Human(GRCh38) and click the GO button.
This format also works: chr22:18217079,chr22:18220831,chr22:18229556
This query returns the human and mouse BID and Bid genes and phenotypes associated with the mouse gene.
Type alzheimer in the Search by disease or phenotype terms section of the form. If you are interested in a particular type of Alzheimer Disease, then select it from the list that appears. Repeat the process if you wish to include more types. For the broadest search, don't select anything, just click out of the field and click the GO button.
The broadest search finds all diseases and their synonyms that contain the word, Alzheimer, and returns all human genes associated with the disease and mouse genes and transgenes used to model the disease. The grid also displays phenotypes and diseases associated with these mouse genotypes, some of these will have no association with Alzheimer Disease. You can filter the grid to phenotypes and diseases and markers that interest you by checking the appropriate row and column boxes and clicking the Apply Filters button. This also applies the filters to both the Genes and Diseases Tabs.
Type MP:0012315 AND NOT Alzheimer in the Search by disease or phenotype terms section of the form. The Effective Phenotype Query will show:
(impaired learning - MP:0012315 AND (NOT Alzheimer))
The search finds mouse genes with alleles annotated to the term, impaired learning, and its subterms and shows the genes' human homologs and all high level terms and human diseases also annotated to the alleles.
- Click the Export: Text File button.
- Open the file in your spreadsheet software application and copy either the Marker Symbols or IDs.
- Direct your web browser to the MGI Batch Query and paste the markers into the text field.
- Check the Gene Attributes you wish to see in your results.
- In the Additional Information section, select Gene Ontology (GO) to find functional information.
- Click the Search button.
The results show GO IDs and terms that describe the biological processes, molecular functions and cellular components of the gene products. The Batch Query only provides data for mouse genes. If you searched with human gene symbols, synonyms or IDs, the search will return data for their mouse homologs.