More Help

This Help document answers the following questions about interpreting the Mammalian Orthology Query Results :

• What's in the Mammalian Orthology Query Results?
• How do I view resources for genes or sequences?
• How do I download sequences in FASTA format?
• How do I forward sequences to MouseBLAST?
• How do the buttons work? What does Invert do?
• How do I interpret these results?
• Are there any supporting references?
• Are there any comparative maps?

See also:

• MGI Glossary (for unfamiliar terms or acronyms)

What's in the Mammalian Orthology Query Results?

The Mammalian Orthology Query Results page contains:

• a table summarizing orthology information on the gene
• the ability to select sequences from that table for downloading in FASTA format or forwarding to MouseBlast
• a column of all known species with orthologous genes
• links via the database accession identifier to the sequence source
• a column of evidence codes for each orthology assertion
• links to the supporting references for the assertions
• links to a comparative map displaying all genes/markers within 2 centiMorgans of the gene or marker of interest
• additional references for all evidence assertions or for selected species
• links to additional resources with orthology data for this gene (e.g., Ensembl Gene Tree (phylogenetic trees of animal genes), Protein Superfamily reports, VISTA on UCSC browser (whole genome alignment), Homologene (at NCBI: automated detection of homologs among the annotated genes of completely sequenced eukaryotic genomes), MGI Mouse-Human-Rat Comparative GO Graph (curated GO classifications for mouse, human and rat orthologs annotated from the biomedical literature).

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How do I view the resources for genes or sequences?

A Mammalian Orthology Query Results table displays, by species, external gene resources and/or MGI-stored sequences for your query. To access:

• Locate the item of interest in the AccID (Source) column.
• Click the desired provider link (e.g., HGNC, Entrez Gene, RefSeq, Uniprot, OMIM).
  The provider's record for this accession ID appears.

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How do I download sequences in FASTA format?

1. Click to put a check mark in the Select column next to one or more sequences.
2. Ensure that download in FASTA format appears in the box next to For the selected sequences.
3. Click Go. The selected sequences appear on a new page, in FASTA format.

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How do I forward sequences to MouseBLAST?

To forward sequences to MouseBLAST:

1. Click to put a check mark in the Select column next one or more sequences.
2. Click the down arrow in the box beside For the selected sequences.
3. Click forward to MouseBLAST.
4. Click Go.

For additional information, see:

• Using the Forward to MouseBLAST Form
• Interpreting the MouseBLAST Output Report

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How do the buttons work? What does Invert do?

Button	Action	Use this when...
Select all	Puts a check mark into every available check box.	You want to examine each sequence.
Invert	A toggle switch. Removes any check marks and puts them in any boxes not previously selected.	the list you want is longer than the list you do not want. Click Select All, click the undesired sequences, click Invert. you don't want the action of Reset.
Reset	Removes any check marks from boxes.	You want to start over and make all new selections.
Go	Activates your choice (or the default) from the selection menu.	You are ready to download a sequence in FASTA format or forward it to MouseBLAST. See How do I download sequences in FASTA format? or How do I forward sequences to MouseBLAST? for details.

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How do I interpret these results?

For each ortholog in a class, the record shows some or all information in the following table, depending on the information available.

Species | Symbol | Chr (Location) Coordinates | AccID (Source) | Evidence | References (table) | Comparative Map | References (list) | Links

FIELD	DESCRIPTION
Species	Species name of each ortholog in a class.
Symbol	Symbol for an orthologous marker.
Chr (Location) Coordinates	The chromosome the marker is assigned to, and, enclosed in parentheses, the cM position or cytogenetic band. Location information varies depending on information available.
AccID (Source)	Database accession IDs assigned to the marker, linked to the database where the marker record is stored. Currently, MGI stores orthology information from databases such as Ark-Cat, BovMap, Entrez, HGNC, HorseBase, OMIM, PigBase, RGD, SheepBase.
Evidence	MGD orthology information includes criteria for orthology assertions. Criteria are represented as acronyms; possible values include: AA Amino acid sequence comparison CE Coincident expression CL Conserved map location FH Formation of functional heteropolymers FC Functional complementation IX Immunological cross-reaction NS Not specified NT Nucleotide sequence comparison SI Similar response to specific inhibitors SL Similar subcellular location SS Similar substrate specificity SU Similar subunit structure UN Unreviewed XH Cross-hybridization to same molecular probe
References (table)	Each criterion is associated with one or more references. Each evidence column contains a J:number, linked to the particular reference set for the criterion and species.
Comparative Map	Click the desired species (rat, human) to see a 2 cM display around the queried marker.
References (list)	Click Display all or select a species to see all or selected references.
Links	Additional links to databases or resources with orthology data for this gene (e.g., Gene Tree, VISTA, HomoloGene, MGI Protein Superfamily reports, MGI Mouse-Human-Rat Comparative GO Graphs).

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Are there any supporting references?

Yes. Each orthology class represented in the results includes links to supporting references. Beneath the table is the option to display all references for the orthology class or those pertaining to selected species. References are in short citation format and include the following information:

• J number
• Author list
• Title
• Journal
• Publication date
• Volume and pages

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Are there any comparative maps?

Yes. The query results for each orthology class provide a link to a comparative map showing the region within 2 cM of the mouse marker and any orthologies in the selected other species. This link only appears if the query results include mouse markers. The map display is in Web Map format.

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