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This document answers the following questions about the Recombinase Alleles - Tissue Summary page:

• What are the ways of creating different views of the data on this page?
• When does a Recombinase Alleles - Tissue Summary appear?
• What should show up on this page?
• How do I interpret the information on this page?
• Why is the matrix view missing for some alleles?
• How do I filter my results?

See also:

• the Phenotypes, Alleles, and Disease Models Query Form for locating recombinase-containing alleles.
• the Gene Expression Data Query Form to find endogenous gene expression.

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

You can:

• Click column headings to sort table data. The initial sort is alphabetical, A-Z (for most columns). Click the column heading or the arrows to reverse the sort. The exception is the Recombinase Data column which sorts by the total number of systems with data. Again, click the heading to reverse the sort (least to most).
• Click and hold down the mouse on any of the column headings in the lower table to drag that column to the left or right and thereby rearrange the data order. You could, for example, place the Driver column all the way to the right of the lower table.

When does a Recombinase Alleles - Tissue Summary appear?

The Recombinase Alleles Summary presents a table of transgenic, and targeted or endonuclease-mediated knock-in recombinase alleles contained in the MGI database. It appears when you select either a driver or enter an anatomical structure from the boxes on the Recombinase (cre) Activity page and click Search.

What should show up on this page?

The table resulting from a Recombinase Allele Activity query contains a row for either:

• every recombinase allele in the MGI database for the selected driver, whether it has tissue activity data or not.
• only those recombinase alleles in the MGI database having data for the queried anatomical structure.

The data on the Recombinase Alleles - Tissue Activity Summary are information about assays demonstrating the activity of the recombination allele in particular tissues, at or prior to the time when the mouse tissue is assayed. This is referred to as tissue activity or recombinase activity data.

Although all data are captured in MGI's database as expression assays, the assays of type recombinase reporter are more correctly referred to as demonstrating activity of the recombinase allele rather than its expression. This is because tissues where the assay shows recombinase allele activity may be descendants of the tissue (as development and cell differentiation continues) in which the recombinase allele first began producing its protein (began being expressed).

Once the recombinase has acted upon the target gene by removing or rearranging part of its sequence, all descendant tissues will carry the recombined target gene.

Careful analysis of cre activity in the cre transgenic mouse lines is important because low levels of excision early in development may produce only a few cells with cre excision, but all the descendants of those cells will carry the cre-induced genomic alteration.

Assays of type In situ reporter (transgenic) and In situ reporter (knock in) are correctly referred to as expression data because they demonstrate the expression of the recombinase allele at the age when the allele is producing its protein for assays with antibody detection or its mRNA for assays with nucleotide probes. When the specimen's genotype involves a recombinase allele, the results of these expression assays are included in the summary table.

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How do I interpret the information on this page?

The box at the top of the page lets you control the display of the data. See What are the ways of creating different views of the data on this page? for more detail.

• Some or all of the following fields appear, depending on whether you search for recombinase activity in a particular anatomical system or use a promoter to search for tissue activity data.
• You can rearrange table order by clicking a column heading, holding the mouse down, and dragging the column to the left or right.
• You can also rearrange the order in which data appears by clicking the column headers (titles). The initial sort is by driver, alphanumeric A-Z. Click to sort the driver from Z-A.

Driver | Matrix View | Allele Symbol/Gene; Allele Name | Recombinase Activity | Induced By | Find Mice | Refs | Allele Synonym

Field	Description
Driver	Gene, genetic element, or construct that promotes recombination.
Matrix View	If there are recombinase activity data for any allele, a grid icon will appear in this column. The icon links to a matrix which allows you to compare endogenous wild-type gene expression with reported recombinase activity data.
Allele Symbol Gene; Allele Name	Official symbol for the allele, linked to the MGI Detail Report for this allele. Note that the detail page has a Recombinase Activity row listing every system examined where activity has been detected or not detected. Each system links to its activity detail page. Gene name; allele name.
Recombinase Activity Detected	Information about anatomical systems where recombinase activity data was assayed and detected This field will be empty when data showing activity are absent or have not been analyzed. If you searched for activity detected in a structure, the relevant high level system(s) will be in bold text. Click the column heading to sort by anatomical system.
Recombinase Activity Not Detected	Information about anatomical systems where recombinase activity data was absent (not detected), as well as activity that has not been analyzed or recorded in the database for the specified structure This field will be populated only when the absence of activity has been shown. Click the column heading to sort by anatomical system.
Induced By	If treatment (of mice carrying a cre allele) is required to activate recombinase activity, then the inducing agent (e.g. tamoxifen) is shown.
Find Mice (IMSR)	Information about the availability of mouse strains and/or cell lines of this allele in the International Mouse Strain Resource (IMSR).
Refs	Links to MGI Reference reports for all references indexed for the allele.
Allele Synonym	Any additional designations for the allele.

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Why is the matrix view missing for some alleles?

The presence of a grid icon in a row indicates that a Gene Expression + Recombinase Activity Comparison Matrix is available. This matrix compares the endogenous wild type gene expression for the driver gene with the recorded recombinase activity of its alleles. This grid is unavailable when an allele has yet to have recombinase activity recorded in the database.

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How do I filter my results?

You can filter results by Driver, Inducer, Detected in System, or Not Detected in System. In the banner above your results, after Filter alleles by:, click the desired box. This will reduce your results to only those containing the checked items.

If you select more than one system in the Detected in System and Not Detected in System filters, the filtered results will display any result that contains one of the checked systems (the boolean OR result). The results between the different filters apply the boolean AND. For example, if you checked liver and biliary system and renal and urinary system for recombinase Detected in System and endocrine system and hemolymphoid system for recombinase Not Detected in System, this will return results where recombinase was detected in either liver and biliary system OR renal and urinary system AND also Not detected in either endocrine system OR hemolymphoid system.

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