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SEARCH FOR EXPRESSION IN SUBCELLULAR STRUCTURES USING ANTIBODIES

We will look for expression in wild-type fish under standard or control experimental conditions. Subcellular expression is found in the "Subterm" field in the "Expression" data section of ZebrafishMine.

To get started:

Click on the Query Builder tab. When on the Query Builder page, double-click on Expression from the "Select A Data Type to Begin a Query" section:

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Expression will now be visible in the Model Browser window:

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Building the query, step-by-step:

1. Assay (under Expression):  Click on "SHOW" next to Assay. To limit results to immunohistochemistry, click on "CONSTRAIN" next to Assay and select "immunohistochemistry" from the menu. Add to query.
2. Expression found (under Expression): Click on "SHOW".
3. Anatomy: Expand the Anatomy section by clicking on the + to the left of Anatomy. Go to "Name" under Anatomy. Click "SHOW" next to  Name.
4. Antibody: Expand the Antibody section by clicking on the + to the left of Antibody. Go to "Symbol" under Antibody. Click "SHOW" next to  Symbol.
5. Environment: Expand the Environment section by clicking on the + to the left of Environment. Click on "CONSTRAIN" next to Environment. In the window that pops up, fill in ZDB-EXP-041102-1. This is the identifier for Standard environments. Click on "CONSTRAIN" next to Environment once more. In the window that pops up, fill in ZDB-EXP-070511-5. This is the identifier for Generic control environments.
6. Edit environment constraints: We want to find expression in standard or generic control environments, but the Query Builder will add "Standard AND Generic control" by default. To change the "AND" to  "OR", click on the pencil icon at the bottom of the Query Overview section. Change "A and B and C" to "A and (B or C)". Click on "Update".

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7. Gene: Expand the Gene section by clicking on the "+" to the left of Gene. Go to "Symbol" under Gene. Click "SHOW" next to  Symbol.

8. Gene: Change constraint: In the Query Overview, click on the dark blue circle next to "Gene". In the popup, change constraint from the default "Show only Expressions if they have a Gene" to "Show all expressions and show Genes if they are present". Add to query.
9. Genotype: Expand the Genotype section by clicking on the "+" to the left of Genotype. Go to "Geno Display Name". Click on "SHOW" next to "Geno Display Name". Under Genotype, go to "Is Wild Type". Click on "SHOW". Then click on "CONSTRAIN". In the popup window, select "true" and add to query.
10. Subterm: expand the Subterm section by clicking on the "+" to the left of "Subterm". Click on "SHOW" next to "Name", and "SHOW" next to "Namespace". (Note: Subcellular terms are housed in the "Subterm" field).
11: Subterm:Parents: Find "Parents" under "Subterm" and expand by clicking on the "+" next to it. Find "Namespace" under "Parents". Click on "Constrain" next to "Namespace. In the popup menu, select "cellular_component". Add to query.

Run the query by clicking on "Show results".

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Below is the QUERY XML for the above query. You can paste it in the box here and click submit.

<query name="" model="genomic" view="Expression.assay Expression.expressionFound Expression.anatomy.name Expression.antibody.symbol Expression.gene.symbol Expression.genotype.genoDisplayName Expression.genotype.isWildType Expression.subterm.name Expression.subterm.namespace" longDescription="" sortOrder="Expression.assay asc" constraintLogic="A and (B or C) and D and E">
<join path="Expression.gene" style="OUTER"/>
<constraint path="Expression.assay" code="A" op="=" value="Immunohistochemistry"/>
<constraint path="Expression.environment" code="B" op="LOOKUP" value="ZDB-EXP-041102-1" extraValue=""/>
<constraint path="Expression.environment" code="C" op="LOOKUP" value="ZDB-EXP-070511-5" extraValue=""/>
<constraint path="Expression.genotype.isWildType" code="D" op="=" value="true"/>
<constraint path="Expression.subterm.parents.namespace" code="E" op="=" value="cellular_component"/>
</query>

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