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Clicking on the "?" button from any search type will take you to the appropriate help section.

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Gene Search

To search for probes associated with a specific gene, select the Gene Search radio button, type the gene name, gene symbol, Entrez Gene ID or probe name in the search box and click the "Search" button. Alternatively, select a category from the tag cloud. The font size of the words in the cloud correspond to the number of genes linked to each category. Genes were linked to each category using online tools such as the PANTHER.

To restrict the set of probes displayed, check the boxes next to the Gene Symbols and click the View Selection Heatmap button at the bottom of the page (see heat map figure below).

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Differential Search

Another common usage of gene expression databases is to find genes that show enrichment of expression in one region compared to another region. This type of query is supported by the Differential Search mode. Select the "Differential Search" radio button. To find genes or probes with an enhanced gene expression profile in one or more structures when compared to one or more other structures, enter the target brain structure in the top search box and your contrast regions in the bottom search box. You also have the option to filter your search by donor. Once you have made your selections, click on the Search button.

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To perform the previous search in reverse, click the toggle button to the left of the Search button.

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Correlative Search

In using gene expression databases, a "search by example" feature is also highly desirable as genes with similar expression patterns may be related in function. The Find Correlates search utility will accomplish this function. This search by example facility is also available in the Allen Human Brain Atlas, and in the Allen Mouse Brain Atlas and the Allen Developing Mouse Brain Atlas as the NeuroBlast function.

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Only regions selected for the search will be displayed. To see the search results across the entire brain, turn off the "Restrict Domains" function at the bottom of the heat map. You can see "anti-correlated" genes by toggling the sort order on column "r" or scrolling to the bottom of the heat map.

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Gene Classification

When you are viewing heatmap data, there will be a "Gene Classification" radio button available. When the gene classification radio button is selected, you can search for enhanced gene expression from one of the categories in the drop down menu.

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Data Visualization

The visualization page for the prenatal LMD microarray data is divided into two sections:

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