Interpreting Recombinase Activity Details

This help document describes Recombinase Activity Detail reports which contain some or all of the following elements:

• What should appear on this page?
  • Title
  • Allele information
  • Tissue information
  • Images
  • Recombinase activity
  • Assays
  • Genotypic Background
  • Result Notes
  • References
• What are the ways of creating different views of the data on this page?

See also:

• Using Recombinase Alleles - Tissue Activity Summary Reports
• Using the Phenotypes, Alleles, and Disease Models Query Form (recombinase-containing transgenes or knock-ins or floxed or frt alleles)

What should appear on this page?

The Recombinase Activity Detail page summarizes the recombinase expression for the selected allele and tissue combination.

Title

The title on an Recombinase Activity Detail report takes the form:

[allele symbol] - [name of anatomical system ] For example: Foxg1^tm1(cre)Skm - Alimentary System

Fields

The table below describes the possible fields in a Recombinase Activity Detail report. If a field does not appear, it means that information is not currently available for this allele.

Allele information | Tissue information | Images | Recombinase Activity | References

Field	Description
Allele information	Allele The allele symbol is composed of the gene symbol and the allele designation. If the gene is unknown, only the allele designation appears. Driver The gene, gene promoter, or construct. Type Specific allele category: e.g., Targeted (Recombinase), Targeted (Inducible, Recombinase), Transgenic (Recombinase), Transgenic (Inducible, Recombinase) Inducer If treatment (of mice carrying a cre allele) is required to activate recombinase activity, then the inducing agent (e.g. tamoxifen) is shown. Synonym Other names for the allele. Molecular description Details of allele generation. Molecular references cited link to MGI Reference Detail reports. Find Mice (IMSR) Information about the availability of mouse strains and/or cell lines of this allele in the International Mouse Strain Resource (IMSR) and an indicator of whether or not there are any strains or lines available for any allele of this transgene or gene. Additional Tissues Systems in which activity data has been curated. Each system listed links to its own Recombinase Activity Detail page for this allele.
Tissue Information	[system] - On the left, the name of the system with recombinase activity. On the right, other recombinase alleles with activity in that system. Each listed allele links to its MGI Recombinase Activity Detail page in the specified system. If ...(more) appears, click it or the arrow icon () to expand the list.
Images	Any images that the MGI database contains for this combination of allele and system. You can resize each image and drag it anywhere on the page. This is especially useful for side-by-side comparisons of expression in a given structure.
Recombinase Activity	Structure Recombinase activity results are associated with structures described in the Anatomical Dictionary. Structures appear in alphabetical order, A-Z. Click the column name to reverse the order. Cell Type Cell type, if specified. Use of the Cell Type (CL) Ontology for annotation began in 2022, so there are not many annotations using it in the database. Assayed Age Age of the embryo at time of assay. Level Intensity of observed expression as specified by the author(s). Possibilities are: Absent, Present, Ambiguous, Trace, Weak, Moderate, Strong, Very Strong. Present appears if the author does not explicitly describe expression level. Pattern As specified by the author(s), possibilities are: Homogenous, Non-Homogenous, Diffuse, Graded, Patchy, Regionally Restricted, Scattered, Single Cells, Spotted, Ubiquitous, Widespread, Not Specified, Not Applicable. Reference, Source The J number (MGI ID) of the paper with the data, linked to the MGI References Query Results -- Details for the abstract and additional information, the figure number of the Image and a thumbnail of the image. If images and/or data are available from an external web resource, a link will be provided here.
Assays	Click the Assays tab (at the top of the table) to show columns with the assay type; the detection method; the reporter gene, probe or antibody; and notes about the assay. Assay Type In situ reporter (knock in), in situ reporter (transgenic), or Recombinase reporter. Reporter Gene Gene assayed for. Detection Method Assay method. Examples: direct detection, probe, antibody. Assay Note Details pertaining to the entire assay, e.g. treatment.
Genotypic Background	Click the Genotypic Background tab (at the top of the table) to show columns containing the allelic composition, genetic strain background, sex, and notes about the specimen. Allelic Composition, Genetic Background Allele pairs that contribute to the genotype and the mouse strain background. Each allele is linked to its corresponding Phenotypic Allele Detail Report. Beneath the allele pairs, in parentheses, the strain of the genetic background appears; e.g., (involves: 129/Sv * C57BL/6) or (not specified). Involves Indicates that the strains listed (separated by asterisks) contributed to the genetic background of the specimen; additional unspecified strains may also be part of the specimen's genetic background. Either Indicates that more than one genetic background appears in a reference, but the background of the specimen is unspecified. Sex Male or female, when known. Not specified is the most common entry. Specimen Note Provides additional information on the treatment or assay details on individual specimens; for example, maternal/paternal transmission of the cre allele.
Result Notes	Click the Result Notes tab (at the top of the table) to see data about, for example, staining in the assayed tissue, in the Result Note column.
References	All for this allele: Number of and link to the References Query Results -- Summary of all the MGI papers for this allele.

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What are the ways of creating different views of the data on this page?

You can:

• Click Assays to view any available data in these additional columns: Assay Type, Reporter Gene, Detection Method, Assay Note.
• Click Genetic Background to view any available date in these additional columns: Allelic Composition, Genetic Background; Sex; Specimen Notes.
• Click Result Notes to see available data in the Result Note column.
• Click column headings containing up/down arrow icons to resort column content.
• Move images from their original location in the Images table row to any location on the page (for comparison with other images or data).
• Resize an image (in the Images row) by clicking it and dragging its corners.
• Click an image in the Reference, Source column to identify its corresponding larger image in the Images row.

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