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To search for probes associated with a specific gene or group of genes, select the Gene Search radio button and type the gene name, gene symbol, Entrez Gene ID or probe ID in the search box (multiple genes searches require an OR between gene names) before clicking the "Search" button. To show exact matches to your search query click the "Show exact matches only" box.
Boolean Syntax
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To find genes that show enrichment of expression in one region compared to another region, use 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 brain regions when compared to one or more other brain regions by entering the target structure(s) in the top search box (separate structures with a semicolon) and your contrast structure(s) in the bottom search box and click the Search button.
The search returns will show genes exhibiting higher expression in the target region(s) compared to the contrast region(s).Search results are sorted either by p-value or fold change, indicated by the arrow on the buttons over the column of genes. To alter the sort parameter, click on either the "p-value" or the "fold change" button.
To filter your results by structure or by donor, click on the "Filter Heatmap" button below the heatmap.
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For human brain data, microarray data is visualized as a heatmap where each column represents a tissue sample in ontological order. Heatmap color represents the z-score over a probe ranging from green (z-score of -3 and below) through black to red (z-score of +3 and above). Hover over any position in the heatmap to obtain the associated tissue sample structural annotation.
GENE CLASSIFICATION
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Once you have identified a gene of interest, to find other genes with spatial expression profiles similar to your gene of interest, first select your probe by clicking on any cell in the heat map related to that probe. You will see that probe listed in the box above the right hand side of the heat map. Then select the brain structure(s) in which you would like to see a similar expression pattern, and click "Find Correlates". This action will return probes with a similar expression profile to brain region(s) in which you are interested.
You can see "anti-correlated" returns by toggling the sort order on column "r" or scrolling to the bottom of the heatmap.
You can show less data by turning on the "Filter Heatmap" which will bring up a menu that will allow you to select the donors and structures you'd like to see represented in the heatmap.
You can see "anti-correlated" returns by toggling the sort order on column "r" or scrolling to the bottom of the heatmap.
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In the top right hand corner of the heat map is a toggle button, 
which when clicked will sort the heat map data either by donor or by structure.
Data Aggregation and Normalization
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Additional information is shown in the middle panel, and includes gene symbol, gene name, probe name, the log2 expression value and z-score and links to related data in other Allen Brain Atlas resources. Links to donor meta-data are also included in this panel. Blue text indicates a hyperlink, where there is more information available by clicking on the text.
The "Brain Explorer" link, when selected for the first time, will take you to a page where you can download the Brain Explorer® 2 3-D viewer software. Once the Brain Explorer program is loaded, clicking on the "Brain Explorer" icon will launch a desktop software application for viewing the Atlas gene expression data in three dimensions.
The "Planar View" icon launches the multiplanar viewer that shows the expression profile for the selected probe in the context of the donor brain.
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Click the "View Selection Heatmap" button to see all of your selections as a heat map. Alternatively choose “View Selection Thumbnails” to view your selection as 3-D rotating thumbnails.
In “Thumbnails” mode each row represents a probe with data from each donor arranged from left to right. The color patches in the thumbnail represents a physical tissue sample using the same user-specified color scheme as for heatmap viewing. Clicking on a patch will turn it bright blue and bring up detailed information in the area above the thumbnails. To rotate the thumbnail, drag the black downward triangle on the slider labeled “Rotate”. You can switch between viewing left cortical, right cortical and sub cortical samples using the “Left Cortex”, “Right Cortext” and “Subcortex” buttons located above the thumbnails. Cortical samples projected on a standard inflated white matter surface while sub-cortical samples are displayed as spheres in their 3D sampling locations.
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For each probe, we have provided an anatomical abstract view of the gene expression pattern of each donor. Regions of the brain are listed in each of the views, and the text can be removed by clicking on the 'Labels' button. The cortical gene expression patterns (3) are displayed on an inflated cortical surface (outer and inner surfaces of the left hemisphere). Subcortical structures of the brain are represented from a frontal view (4), and subcortical as well as brainstem structures are shown in a side view (5). Hovering your mouse over an annotated structure will bring up the structure name as well as the normalized and raw expression level values. Clicking on a structure will bring up links to the #Multiplanar Viewer and the Brain Explorer.
Multiplanar Viewer
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This screenshot shows the multiplanar navigation controls. Samples from which microarray tissues were assayed are represented as colored boxes on the MR images and show expression level, according to the active color map. Instead of the MR image, you can select a 3-D thumbnail showing the cortical gene expression.
Click or click-and-drag to move the crosshairs on any of the three MRI views ports.
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Image and Probe Navigation
In this screenshot you see the heat map associated with a single, user-defined probe of interest as well as two image viewers illustrating the 2-D histology associated with the point selected by the MRI cross-hairs. The viewer on the left-hand side shows a larger view of the relevant brain slab, with a blue highlight around the block of that slab from which the selected sample was taken. The viewer on the right-hand side shows a detailed view of that block, with structure annotations visible. An arrow on the left hand side of the viewer indicates which direction is dorsal (top of the head).
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