Using the Gene Expression + Recombinase Activity Comparison Matrix
Using the Gene Expression + Recombinase Activity Comparison Matrix
This help document answers the following questions:
The Recombinase Activity Comparison Matrix allows you to compare endogenous wild-type gene expression with reported recombinase activity data.
The official gene symbol, name and MGI accession ID for the gene of interest appear at the top of the page.
The first column shows endogenous wild-type gene expression data for the gene. The following columns show recombinase activity data for recombinase alleles driven by the matching gene. The allele columns are sorted, left to right, by driver species, where alleles with mouse drivers are first (left-most), then human, rat, then other driver species, with "not specified" driver species last (right-most). Within each group, targeted before endonuclease-mediated alleles, then transgenic alleles. Finally, smart alpha on allele symbol within these last groups. The allele column headers link to the appropriate allele detail page. Please note that not all recombinase-carrying alleles are displayed in this matrix. Alleles whose tissue activity data has not yet been recorded are omitted.
The tissues consist of anatomy terms from The Mouse Developmental Anatomy Ontology. You can expand or collapse the anatomy hierarchy by clicking on the blue ► or ▼. Colored cells indicate the presence of data annotations. Click a colored cell to access the supporting data.
For the Expression Data in the first column:
The colors in the grid, blues for recombinase activity detected and reds for recombinase activity not detected, get progressively darker when there are more supporting annotations. The darker colors do not denote higher or lower levels of recombinase activity, just more evidence.
Grey bars indicate the only annotations for the tissue are ones for which the researchers examined the tissue but did not definitively state whether recombinase activity was present or absent, i.e. their description was ambiguous.
Cells with a red corner indicate that recombinase activity has been reported as being both present and absent in that tissue. Although this may be because different labs made conflicting observations, it may also be due to other factors, such as differences in the genotype or sex of the specimen, sensitivity of the assay used, or a difference in the transcript variant assayed.
A white cell with a gold corner indicates that although there are no annotations where recombinase activity was reported as being present in either the tissue or its substructures, there are recombinase activity results for substructures of the tissue that were reported as being either absent or ambiguous. See How are expression results propagated through the matrix anatomy hierarchy?
A circle in a cell indicates the tissue exists at that Theiler stage but we have no recombinase activity data for it, whereas a blank cell indicates that the tissue does not exist at that stage.
Clicking in any box in the grid will open a dialogue box. For blue cells, this box will indicate the number of annotations where recombinase activity was reported as being present in either the tissue or its substructures. It may also indicate additional recombinase activity results annotated to this tissue that were reported as being either absent or ambiguous; absent or ambiguous annotations to substructures will not be reported. See How are expression results propagated through the matrix anatomy hierarchy?
A blue cell with a gold corner indicates the structure has both present and absent and/or ambiguous results in substructures.
For red cells, this box will indicate the number of annotations where recombinase activity was reported as being absent in the tissue; annotations to substructures will not be reported. See How are expression results propagated through the matrix anatomy hierarchy?
For grey bars, this box will indicate the number of annotations to the tissue where the recombinase activity levels were reported in an ambiguous fashion. It may also indicate additional recombinase activity results annotated to this tissue that were reported as being absent. In neither case will absent and/or ambiguous annotations to substructures be reported. See How are expression results propagated through the matrix anatomy hierarchy?
Since cells with a gold corner indicate that all the recombinase activity results are absent or ambiguous annotations to substructures (rather than the structure represented by the cell) the number of annotations is not indicated in the dialogue box.
Clicking "View All Results" in a cell's pop-up for the recombinase activity column will take you to the Allele Detail page.
For the Recombinase Activity Data in the second (and subsequent) columns:
Colored cells indicate recombinase activity annotations for the allele/transgene in the column header. The cell colors and other symbols used are the same as those used in the first, gene expression column (i.e. shades of blue indicate tissues with reported recombinase activity, red indicates lack of activity, etc.)
As in the expression column, clicking on a cell for any alleles/transgene column will open a pop-up that reports the number and type of recombinase activity annotations for that tissue. Clicking "View All Results" in the pop-up will link to the allele/transgene detail page where you can view a summary table of all recombinase activity data for the allele/transgene and see if stocks are available in through the International Mouse Strain Resource (IMSR).
The nature of the expression/recombinase activity data requires present and absent results to be managed differently in the matrix anatomy hierarchy. From the statement, "expression/recombinase activity was detected in the heart ventricle," we can infer that "expression/recombinase activity is detected (somewhere) in the heart." In contrast, the statement "expression/recombinase activity was not detected in the heart ventricle" does not imply that "expression is found (nowhere else) in the heart." Therefore, not only is a positive result is displayed in the matrix as a blue square for that anatomical structure, but any parent structure will also display a blue square based on that present result. In contrast, absent results can only be represented for that structure in the matrix. Parent structures will not display a red square based on an absent result in a child structure.
Rows under a system section show direct annotations counts only, while system level rows show the sum of counts in their sections.
Not all recombinase-carrying alleles are displayed in this matrix. Alleles whose tissue activity data has not yet been recorded are omitted.
There are three ways to access this matrix: