Microarray Data

The Data Set

The website offers three types of searches to allow a user to: (1) limit the visualization to a subset of probes (or genes) of interest (Gene Search); (2) use a 'seed' gene to find other genes with similar expression patterns (Find Correlates); and (3) compare expression between different anatomic regions (Differential Search).

Gene Search

To search for a gene category by disease, pathway, cell type or function, click on the relevant search term in the tag cloud. 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 or Entrez Gene ID in the search box (multiple genes searches require an OR between gene names) before clicking the Search button.

Boolean Syntax

The following special operators can be used to build queries:

• AND, OR and NOT may be used in place of their corresponding operators. They must be upper case.
• The AND operator (&) is implicit, so spaces between words that are not separated by an operator will be treated like an &.
• OR (|) has higher operator precedence than AND (&).
• Parenthesis can be used to group criteria, but nested parenthesis are not supported at this time.
• The NOT operator (!)is not supported within parenthesis.

Return to Contents

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 Mouse Brain Atlas, Allen Developing Mouse Brain Atlas and BrainSpan: Atlas of the Developing Human Brain.

To find other genes with 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.

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" returns by toggling the sort order on column "r" or scrolling to the bottom of the heatmap.

Return to Contents

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 a higher expression in one structure when compared to another structure, enter the target brain structure in the top search box and your contrast region in the bottom search box and click on the Search button.

Your search will return results in the two brain regions selected. The results will show higher expression in the target region compared to the contrast region. (To view the expression patterns of the returned probes over the entire brain, turn off the "Restrict Domains" function below the heat map.) 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" buttons.

To perform the previous search in reverse, click the toggle button beside the Search button.

Return to Contents

Data Visualization

Based on your search, the resulting microarray data sets are presented as a matrix with brain structure (by individual donor) on the horizontal x-axis and gene probes on the vertical y-axis. The microarray data is presented in a "heat map" format where the colors of the heat map correspond either to raw data or to a normalized (z-score) expression level of a probe. Brain structures are organized such that moving left to right on the x-axis is analogous to moving from anterior to posterior first in the cortical areas, followed by subcortical areas, cerebellum and brainstem.

Data Aggregation and Normalization

Unless viewing data from a single sample, the heat maps presented on this site are based on data aggregated within brain structures ("Averaged Samples", see below). That is, when there are multiple samples for a given structure, the value represented in the heat map will be the average of those sample values.

We further aggregate the expression values up the ontology tree, i.e. Frontal Lobe, will have a single averaged expression value, which is the average value for all samples belonging to the Frontal Lobe.

Data represented in the heat maps has been normalized across the entire data set before it is aggregated, and is normalized again for each probe when the heat map is constructed.

Heat Maps

The "heat map" is a visualization of the microarray values for the returned probes of interest. Each row of the heat map represents a probe. Each column of the heat map either represents a tissue sample or anatomical brain structure depending on the selected Resolution (Coarse, Averaged Samples, or Sample). The colors of the heat map are normalized expression values. Default heat map colors are in the green – red scale where the color green should be interpreted as relatively low expression and red as relatively high expression within the scope of each probe.

The color map used for the heat map display can be changed to suit the user. You can use the color map bar at the bottom of the heat map to display different normalized (z-score) color representations of the heat map data (i.e. blue-red vs. green-red)or you can visualize log2 normalized expression map where the color scale ranges from dark blue, representing low expression, and passes through cyan, yellow, orange and finally to dark red, representing high expression.

Clicking on a cell of the heat map will bring up detailed information in the area above the heat map. In the panel on the left, information about the sampled anatomical structure is displayed. The stack of structures represents the hierarchy from the structure ontology. For more details on the ontology see Ontology and Nomenclature, or the Help section on the ontology viewer here.

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 Institute projects. 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 Brain Explorer® 2. Once Brain Explorer 2 is loaded, clicking on the Brain Explorer link will launch a desktop software application for viewing the Atlas gene expression data in three dimensions.

The "Planar View" link launches the multiplanar viewer that shows the expression profile for the selected probe in the context of the donor brain.

The columns of the heat map have a different meaning depending on the selected Resolution. There are three options available from the drop-down menu under the heat map: Coarse, Averaged Samples and Samples. If "Samples" is selected there is a one-to-one correspondence between a column and a physical tissue sample. In the Atlas, there are typically multiple samples for each structure of interest. This oversampling may provide information on variability and spatial gradients. In "Averaged Samples" mode, all samples belonging to the same designated structure are combined and averaged together. In "Coarse" mode, the brain is divided into approximately 20 large neuroanatomic divisions or regions (e.g. frontal lobe, occipital lobe, striatum, dorsal thalamus, ventral thalamus, etc.). Samples within each partition are averaged together to provide a summary value for the partition.

Data from multiple brains may be viewed in two ways. By default, columns are grouped first by donors then by structures, allowing a user to compare the expression profile of the individual brains side-by-side. Grouping the columns initially by structures then by donors allows a user to mix the data of the brains in the dataset within a combined brain structure profile. You can toggle between the two groupings by clicking the toggle button over the scroll bar.

Comparing Genes of Interest

You can add probes of interest to a collection for later viewing. Check the checkbox at the left end of a search result row to add it to your collection. Your choices are stored in a browser 'cookie' on your computer and will remain in effect until you click the 'Clear Selections' button, or clear your web browser's cookie cache.

Click the 'View Selections' button to see all of your selections.

Please note that this feature requires that you have cookies enabled in your browser, which is already the case for the great majority of users.#Return to top

Return to Contents

Gene Detail

Clicking on the Gene Name or Gene Symbol of your Search results will take you to the Microarray Gene Detail page.

The Microarray Gene Detail page displays information about the gene including Organism, Chromosome, Entrez Gene ID, related data from other Allen Brain Atlas resources, Gene Name and Alternate Symbols. Detailed expression heat maps for each probe are stacked by donor for a direct comparison between brains. There is also a section of links to External Resources.

Return to Contents

Probe Detail

Clicking on the Probe Name will take you to the Microarray Probe Detail page.

The Microarray Probe Detail page displays information about the probe including Probe ID, Gene Symbol, Gene Name, Probe Name, NCBI Accession and GI numbers. It also includes the probe type, length, GC percent and sequence information. Detailed expression heat maps from each donor brain are stacked so as to directly compare the probe between brains. There is also a section of links to External Resources.

Return to Contents

Brain Explorer 2 Application

Brain Explorer 2 is a desktop software application for viewing human neuroanatomy and the Allen Human Brain Atlas microarray gene expression data in the framework of the Magnetic Resonance Images of the sampled brains.

Once you have chosen a gene of interest (by clicking on the heat map), you can explore a three dimensional representation of its gene expression by clicking on the "Brain Explorer" link over the heat map. When Brain Explorer opens, you will be taken to a screen that displays the Image Viewer, the Structure Ontology Viewer, and the Gene List.

Image Viewer

The Image Viewer will automatically show the 3D expression representations of your gene of interest on every sampled brain. Cortical gene expression is overlaid on an inflated white matter surface for each donor brain, with spots under the white surface representing gene expression in the subcortical regions of the brain. A striped expression pattern on the cortical surface is a result of having sampled from every other slab of cortical tissue. Under each representative brain is the heat map for the probe you selected. Clicking on that heat map will pinpoint the area in the brain from which the sample was taken.

The gene expression colors correspond to the settings in the Atlas with which you were viewing the original heat map. To change the gene expression representation, click on the "Gene" tab in the top left hand corner of your screen and choose either z-score or raw data representations of the gene expression data.

A compass in the right hand corner of the image viewer depicted by a stylized head can be used to rotate the brains by clicking and dragging your cursor. You can look at a single brain by clicking on the magnifying glass above that brain. Choosing a data point, either by clicking on the heat map below the brain or on a brain region itself, will bring up the gene symbol, the location of the sample and the expression level and z-score in the left hand corner of the Image Viewer.

You can zoom using either the wheel on your mouse or using the Zoom scrollbar in the lower right hand corner of the Image Viewer.

Structure Ontology Viewer

The Structure Ontology Viewer shows the entire collapsible ontology for the human brain including the color coding used by our expert annotation team to visualize structural boundaries. Two columns to the right of the ontology determine the type of data displayed in the Image Viewer. "A" represents annotation and when checked, will show a visual representation of that structure in the Image Viewer. "G" represents gene expression and when checked, will show gene expression in that structural domain.

The default organization for the Structure Ontology is the Hierarchical View, but if you are unfamiliar with the ontology, you can click on the Alphabetical View to see the structure list in alphabetical order.

The Bookmarks tab is a space where you can create and save favorite views of the brain. Several default views are already saved that will rotate the brain back into common viewing frames.

Gene List

This section displays the gene probes you have selected and downloaded in this session. When more than one gene probe has been downloaded, clicking on one probe will show its gene expression profile in the image viewer. Right clicking on the gene probe name will bring up a menu where you can view the gene detail page (Get Info), be taken to the Multiplanar View of the probe (View Images) or copy the gene information for use in another application.

Toolbar

Advanced Features

Atlas Tab:

You can show opaque three dimensional structures of the brain by "showing" or "hiding" structures from this menu. The "Transparent" function allows you to see transparent views of the structures to view the anatomical relationships between them.

Selecting the sagittal, coronal or horizontal sections (or clicking on one of the section image buttons in the toolbar) will superimpose a single plane of the MRI images from each brain on your image space. These planes can be moved once the selection tool mode button in the toolbar is selected. Selecting "Show Annotation on Section" from this menu will color the MRI images according to the brain structure ontology.

Gene Tab:

When you have a gene selected, the Gene Tab menu allows to you to show all expression, hide all expression (for instance to then select a single structure) or toggle expression (for instance, unselect your region of interest then toggle to see expression in only that region).

You can also show or remove threshold controls and choose the visual representation of your data (raw data vs. z-score) from this menu.

To be taken to the gene detail page, select "Get Info". To see the Multiplanar view, choose "View Images". These functions are also available by right-clicking on the gene name in the Gene List.

Clipping Planes:

When this function is selected, either by toggling the cutting tools button in the toolbar or selecting "Clipping Planes" from the View drop down menu, you can make coronal, sagittal or horizontal cuts in your view of the brain and related data. To cut in a particular plane, make sure the cursor is in selection tool mode, and then click and drag on the plane you are interested in clipping.

Return to Contents

Multiplanar Viewer

The Multiplanar Viewer shows sampling sites for microarray data and indicates gene expression levels for a single probe in coronal, sagittal and horizontal sections of MRI space for a given specimen. Additional viewing frames show spatially correspondent histological data at the slab and block level with anatomic annotations and specific delineations of sampling sites for microarray data generation.

Multiplanar Navigation

In the image to right you see the Multiplanar navigation controls. Points from which microarray tissues samples were taken are colored to show expression level, according to the active color map.

Click or click-and-drag to move the crosshairs on any of the three MRI views ports.

The various control and feedback components are labeled here 1 - 7:

1. Donor: Identifier of the donor currently displayed in the viewer.
2. Probe Name: The label for the probe currently displayed in the viewer.
3. Permalink: Click the permalink component to generate a URL that will bring you back to this page with the current location settings.
4. Contrast: Click and drag to move the contrast control.
5. Brain Structure: This field is updated to indicate the structure under the crosshairs. Click on the structure label to launch the ontology browser in a new window.
6. Expression Level: This component reports both the raw expression value and its z-score-normalized value.
7. Color Map Window & Level: adjust the upper & lower bounds, or slide the entire control to modify the range of colors used to map expression levels.

Image and Probe Navigation

In the image at left you see the 2D images associated with the point selected by the MRI crosshairs. The viewer on the left hand shows a larger view of the brain specimen, with a blue highlight around the chunk of that specimen from which the current sample was taken. The viewer on the right hand shows a detailed view of that chunk, with structure annotations visible.

You can navigate from the image viewers as well. The strip of thumbnail images at the bottom of each viewer shows all of the images from its parent specimen, in sectioning order. Clicking on a thumbnail image in the left hand viewer will move the MRI crosshairs and open a new set of images in the right hand viewer. Click on one of the structures to move the MRI crosshairs to the location where that structure was sampled. As you move your mouse over the structures in the right hand viewer its name will appear in the upper-left corner of the viewer.

Use the toolbar icons to add or remove structure annotations such as structure outline, structure colors, and structure labels. To show all specimen images from this block in order, including the Nissl, ISH, SMI-32 and pre- and post-cut LCM images, click . To see the block face images, click . Use the full-page viewer icon to launch a new full-page viewer in a new window for the current image set.

Return to Contents